input is list or vector of taxon names
We can process a single taxon:
-query1 <- make_datelife_query(input = "Canis")
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Making a DateLife query.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================================================================| 100%
-#> ---> Working with the following taxon: Canis.
-#> DateLife query made!
+query1 <- make_datelife_query(input = "Canis")
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Making a DateLife query.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================================================================| 100%
+#> ---> Working with the following taxon: Canis.
+#> DateLife query made!Or several taxon names:
-query10 <- make_datelife_query(input = rep("Canis", 10))
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Making a DateLife query.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================================================================| 100%
-#> ---> Working with the following 10 taxa: Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis.
-#> DateLife query made!
+query10 <- make_datelife_query(input = rep("Canis", 10))
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Making a DateLife query.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================================================================| 100%
+#> ---> Working with the following 10 taxa: Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis.
+#> DateLife query made!In any case, the output is a list:
query10
@@ -140,120 +134,98 @@ When input
The function returns NA as taxonomic id for the missing
name:
-make_datelife_query2(input = c("Canis", "werewolf", "jupiter"))
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================= | 33%
-#> Warning: werewolf are not matched
-#>
- |
- |=============================================== | 67%
-#> Warning: jupiter are not matched
-#>
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Canis" "werewolf" "jupiter"
-#>
-#> $tnrs_names
-#> [1] "Canis" NA NA
-#>
-#> $ott_ids
-#> [1] 372706 NA NA
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
+
+make_datelife_query2(input = c("Canis", "werewolf", "jupiter"))
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================= | 33%
+#> Warning: werewolf are not matched
+#> | |=============================================== | 67%
+#> Warning: jupiter are not matched
+#> | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Canis" "werewolf" "jupiter"
+#>
+#> $tnrs_names
+#> [1] "Canis" NA NA
+#>
+#> $ott_ids
+#> [1] 372706 NA NA
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"
make_datelife_query2(input = "Canis mesomelas elongae")
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Canis mesomelas elongae"
-#>
-#> $tnrs_names
-#> [1] "Canis mesomelas elongae"
-#>
-#> $ott_ids
-#> [1] 576165
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
-
-all_subspecies <- c("Canis mesomelas elongae", "Canis mesomelas elongae")
-make_datelife_query2(input = all_subspecies)
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
-#>
-#> $tnrs_names
-#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
-#>
-#> $ott_ids
-#> [1] 576165 576165
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
-
-one_subspecies <- c("Canis mesomelas elongae", "Canis adustus", "Lycalopex fulvipes")
-make_datelife_query2(input = one_subspecies)
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================= | 33%
- |
- |=============================================== | 67%
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Canis mesomelas elongae" "Canis adustus"
-#> [3] "Lycalopex fulvipes"
-#>
-#> $tnrs_names
-#> [1] "Canis mesomelas elongae" "Canis adustus"
-#> [3] "Lycalopex fulvipes"
-#>
-#> $ott_ids
-#> [1] 576165 621176 996573
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
+make_datelife_query2(input = "Canis mesomelas elongae")
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Canis mesomelas elongae"
+#>
+#> $tnrs_names
+#> [1] "Canis mesomelas elongae"
+#>
+#> $ott_ids
+#> [1] 576165
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"
+
+all_subspecies <- c("Canis mesomelas elongae", "Canis mesomelas elongae")
+make_datelife_query2(input = all_subspecies)
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
+#>
+#> $tnrs_names
+#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
+#>
+#> $ott_ids
+#> [1] 576165 576165
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"
+
+one_subspecies <- c("Canis mesomelas elongae", "Canis adustus", "Lycalopex fulvipes")
+make_datelife_query2(input = one_subspecies)
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Canis mesomelas elongae" "Canis adustus"
+#> [3] "Lycalopex fulvipes"
+#>
+#> $tnrs_names
+#> [1] "Canis mesomelas elongae" "Canis adustus"
+#> [3] "Lycalopex fulvipes"
+#>
+#> $ott_ids
+#> [1] 576165 621176 996573
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"For example, when referring to the grass, TNRS chooses the correct taxon id:
-make_datelife_query2(input = c("Aotus", "Poa", "Arabidopsis"))
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================= | 33%
- |
- |=============================================== | 67%
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Aotus" "Poa" "Arabidopsis"
-#>
-#> $tnrs_names
-#> [1] "Aotus (genus in kingdom Archaeplastida)"
-#> [2] "Poa"
-#> [3] "Arabidopsis"
-#>
-#> $ott_ids
-#> [1] 559026 985636 309275
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
+make_datelife_query2(input = c("Aotus", "Poa", "Arabidopsis"))
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Aotus" "Poa" "Arabidopsis"
+#>
+#> $tnrs_names
+#> [1] "Aotus (genus in kingdom Archaeplastida)"
+#> [2] "Poa"
+#> [3] "Arabidopsis"
+#>
+#> $ott_ids
+#> [1] 559026 985636 309275
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"But when referring to the monkey, TNRS still chooses the grass:
-make_datelife_query2(input = c("Aotus", "Insulacebus", "Microcebus"))
-#> ---> Phylo-processing 'input'.
-#> * 'input' is not a phylogeny.
-#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
-#>
- |
- | | 0%
- |
- |======================= | 33%
- |
- |=============================================== | 67%
- |
- |======================================================================| 100%
-#> $cleaned_names
-#> [1] "Aotus" "Insulacebus" "Microcebus"
-#>
-#> $tnrs_names
-#> [1] "Aotus (genus in kingdom Archaeplastida)"
-#> [2] "Insulacebus"
-#> [3] "Microcebus"
-#>
-#> $ott_ids
-#> [1] 559026 6145234 734824
-#>
-#> $phy
-#> [1] NA
-#>
-#> attr(,"class")
-#> [1] "datelifeQuery"
+make_datelife_query2(input = c("Aotus", "Insulacebus", "Microcebus"))
+#> ---> Phylo-processing 'input'.
+#> * 'input' is not a phylogeny.
+#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
+#> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%
+#> $cleaned_names
+#> [1] "Aotus" "Insulacebus" "Microcebus"
+#>
+#> $tnrs_names
+#> [1] "Aotus (genus in kingdom Archaeplastida)"
+#> [2] "Insulacebus"
+#> [3] "Microcebus"
+#>
+#> $ott_ids
+#> [1] 559026 6145234 734824
+#>
+#> $phy
+#> [1] NA
+#>
+#> attr(,"class")
+#> [1] "datelifeQuery"To make sure that we get the taxonomic id and data for the taxon we want, we can specify a “taxonomic context”:
@@ -334,453 +292,440 @@Choosing between homonymsMaking a query from an inclusive taxonomic group
You can run it for one taxon name only:
-+make_datelife_query2(input = "Canis", - get_spp_from_taxon = TRUE, - reference_taxonomy = "ott") -#> ---> Phylo-processing 'input'. -#> * 'input' is not a phylogeny. -#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). -#> - | - | | 0% - | - |======================================================================| 100% -#> ---> Getting species for the following taxon names :Canis. -#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. -#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. -#> * There are 21 subspecies. -#> * There are 42 total species. -#> * There are 36 species in OpenTree's synthetic tree. -#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. -#> $cleaned_names -#> [1] "Canis" -#> -#> $tnrs_names -#> 3612500 5835572 -#> "Canis dirus" "Canis anthus" -#> 113383 752755 -#> "Canis rufus" "Canis simensis" -#> 621168 621176 -#> "Canis aureus" "Canis adustus" -#> 247331 346723 -#> "Canis latrans" "Canis himalayensis" -#> 346728 4941918 -#> "Canis indica" "Canis environmental sample" -#> 7655930 7655947 -#> "Canis ameghinoi" "Canis nehringi" -#> 7655949 7655942 -#> "Canis palustris" "Canis lanka" -#> 7655948 7655939 -#> "Canis pallipes" "Canis gezi" -#> 7655951 7655935 -#> "Canis primaevus" "Canis chrysurus" -#> 7655937 7655941 -#> "Canis dukhunensis" "Canis kokree" -#> 7655952 7655940 -#> "Canis sladeni" "Canis himalaicus" -#> 7655934 7655936 -#> "Canis chanco" "Canis curvipalatus" -#> 7655943 7655931 -#> "Canis lateralis" "Canis argentinus" -#> 7655953 7655946 -#> "Canis tarijensis" "Canis naria" -#> 7655950 7655933 -#> "Canis peruanus" "Canis cautleyi" -#> 7655954 6145382 -#> "Canis ursinus" "Canis antarticus" -#> 6145383 7655938 -#> "Canis dingo" "Canis etruscus" -#> 666235 247341 -#> "Canis mesomelas" "Canis lupus" -#> -#> $ott_ids -#> Canis dirus Canis anthus -#> 3612500 5835572 -#> Canis rufus Canis simensis -#> 113383 752755 -#> Canis aureus Canis adustus -#> 621168 621176 -#> Canis latrans Canis himalayensis -#> 247331 346723 -#> Canis indica Canis environmental sample -#> 346728 4941918 -#> Canis ameghinoi Canis nehringi -#> 7655930 7655947 -#> Canis palustris Canis lanka -#> 7655949 7655942 -#> Canis pallipes Canis gezi -#> 7655948 7655939 -#> Canis primaevus Canis chrysurus -#> 7655951 7655935 -#> Canis dukhunensis Canis kokree -#> 7655937 7655941 -#> Canis sladeni Canis himalaicus -#> 7655952 7655940 -#> Canis chanco Canis curvipalatus -#> 7655934 7655936 -#> Canis lateralis Canis argentinus -#> 7655943 7655931 -#> Canis tarijensis Canis naria -#> 7655953 7655946 -#> Canis peruanus Canis cautleyi -#> 7655950 7655933 -#> Canis ursinus Canis antarticus -#> 7655954 6145382 -#> Canis dingo Canis etruscus -#> 6145383 7655938 -#> Canis mesomelas Canis lupus -#> 666235 247341 -#> -#> $phy -#> [1] NA -#> -#> attr(,"class") -#> [1] "datelifeQuery"+make_datelife_query2(input = "Canis", + get_spp_from_taxon = TRUE, + reference_taxonomy = "ott") +#> ---> Phylo-processing 'input'. +#> * 'input' is not a phylogeny. +#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). +#> | | | 0% | |======================================================================| 100% +#> ---> Getting species for the following taxon names :Canis. +#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. +#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. +#> * There are 21 subspecies. +#> * There are 42 total species. +#> * There are 36 species in OpenTree's synthetic tree. +#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. +#> $cleaned_names +#> [1] "Canis" +#> +#> $tnrs_names +#> 3612500 5835572 +#> "Canis dirus" "Canis anthus" +#> 113383 752755 +#> "Canis rufus" "Canis simensis" +#> 621168 621176 +#> "Canis aureus" "Canis adustus" +#> 247331 346723 +#> "Canis latrans" "Canis himalayensis" +#> 346728 4941918 +#> "Canis indica" "Canis environmental sample" +#> 7655930 7655947 +#> "Canis ameghinoi" "Canis nehringi" +#> 7655949 7655942 +#> "Canis palustris" "Canis lanka" +#> 7655948 7655939 +#> "Canis pallipes" "Canis gezi" +#> 7655951 7655935 +#> "Canis primaevus" "Canis chrysurus" +#> 7655937 7655941 +#> "Canis dukhunensis" "Canis kokree" +#> 7655952 7655940 +#> "Canis sladeni" "Canis himalaicus" +#> 7655934 7655936 +#> "Canis chanco" "Canis curvipalatus" +#> 7655943 7655931 +#> "Canis lateralis" "Canis argentinus" +#> 7655953 7655946 +#> "Canis tarijensis" "Canis naria" +#> 7655950 7655933 +#> "Canis peruanus" "Canis cautleyi" +#> 7655954 6145382 +#> "Canis ursinus" "Canis antarticus" +#> 6145383 7655938 +#> "Canis dingo" "Canis etruscus" +#> 666235 247341 +#> "Canis mesomelas" "Canis lupus" +#> +#> $ott_ids +#> Canis dirus Canis anthus +#> 3612500 5835572 +#> Canis rufus Canis simensis +#> 113383 752755 +#> Canis aureus Canis adustus +#> 621168 621176 +#> Canis latrans Canis himalayensis +#> 247331 346723 +#> Canis indica Canis environmental sample +#> 346728 4941918 +#> Canis ameghinoi Canis nehringi +#> 7655930 7655947 +#> Canis palustris Canis lanka +#> 7655949 7655942 +#> Canis pallipes Canis gezi +#> 7655948 7655939 +#> Canis primaevus Canis chrysurus +#> 7655951 7655935 +#> Canis dukhunensis Canis kokree +#> 7655937 7655941 +#> Canis sladeni Canis himalaicus +#> 7655952 7655940 +#> Canis chanco Canis curvipalatus +#> 7655934 7655936 +#> Canis lateralis Canis argentinus +#> 7655943 7655931 +#> Canis tarijensis Canis naria +#> 7655953 7655946 +#> Canis peruanus Canis cautleyi +#> 7655950 7655933 +#> Canis ursinus Canis antarticus +#> 7655954 6145382 +#> Canis dingo Canis etruscus +#> 6145383 7655938 +#> Canis mesomelas Canis lupus +#> 666235 247341 +#> +#> $phy +#> [1] NA +#> +#> attr(,"class") +#> [1] "datelifeQuery"Or two or more:
-+make_datelife_query2(input = c("Canis", "Elephas"), - get_spp_from_taxon = TRUE, - reference_taxonomy = "ott") -#> ---> Phylo-processing 'input'. -#> * 'input' is not a phylogeny. -#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). -#> - | - | | 0% - | - |=================================== | 50% - | - |======================================================================| 100% -#> ---> Getting species for the following taxon names :Canis, Elephas. -#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. -#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. -#> * There are 21 subspecies. -#> * There are 42 total species. -#> * There are 36 species in OpenTree's synthetic tree. -#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. -#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. -#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. -#> * There are 5 subspecies. -#> * There are 8 total species. -#> * There are 7 species in OpenTree's synthetic tree. -#> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree. -#> $cleaned_names -#> [1] "Canis" "Elephas" -#> -#> $tnrs_names -#> 3612500 5835572 -#> "Canis dirus" "Canis anthus" -#> 113383 752755 -#> "Canis rufus" "Canis simensis" -#> 621168 621176 -#> "Canis aureus" "Canis adustus" -#> 247331 346723 -#> "Canis latrans" "Canis himalayensis" -#> 346728 4941918 -#> "Canis indica" "Canis environmental sample" -#> 7655930 7655947 -#> "Canis ameghinoi" "Canis nehringi" -#> 7655949 7655942 -#> "Canis palustris" "Canis lanka" -#> 7655948 7655939 -#> "Canis pallipes" "Canis gezi" -#> 7655951 7655935 -#> "Canis primaevus" "Canis chrysurus" -#> 7655937 7655941 -#> "Canis dukhunensis" "Canis kokree" -#> 7655952 7655940 -#> "Canis sladeni" "Canis himalaicus" -#> 7655934 7655936 -#> "Canis chanco" "Canis curvipalatus" -#> 7655943 7655931 -#> "Canis lateralis" "Canis argentinus" -#> 7655953 7655946 -#> "Canis tarijensis" "Canis naria" -#> 7655950 7655933 -#> "Canis peruanus" "Canis cautleyi" -#> 7655954 6145382 -#> "Canis ursinus" "Canis antarticus" -#> 6145383 7655938 -#> "Canis dingo" "Canis etruscus" -#> 666235 247341 -#> "Canis mesomelas" "Canis lupus" -#> 7654243 7654244 -#> "Elephas armeniacus" "Elephas namadicus" -#> 7654245 3607197 -#> "Elephas zulu" "Elephas bombifrons" -#> 6144032 7654246 -#> "Elephas celebensis" "Palaeoloxodon lomolinoi" -#> 541928 -#> "Elephas maximus" -#> -#> $ott_ids -#> Canis dirus Canis anthus -#> 3612500 5835572 -#> Canis rufus Canis simensis -#> 113383 752755 -#> Canis aureus Canis adustus -#> 621168 621176 -#> Canis latrans Canis himalayensis -#> 247331 346723 -#> Canis indica Canis environmental sample -#> 346728 4941918 -#> Canis ameghinoi Canis nehringi -#> 7655930 7655947 -#> Canis palustris Canis lanka -#> 7655949 7655942 -#> Canis pallipes Canis gezi -#> 7655948 7655939 -#> Canis primaevus Canis chrysurus -#> 7655951 7655935 -#> Canis dukhunensis Canis kokree -#> 7655937 7655941 -#> Canis sladeni Canis himalaicus -#> 7655952 7655940 -#> Canis chanco Canis curvipalatus -#> 7655934 7655936 -#> Canis lateralis Canis argentinus -#> 7655943 7655931 -#> Canis tarijensis Canis naria -#> 7655953 7655946 -#> Canis peruanus Canis cautleyi -#> 7655950 7655933 -#> Canis ursinus Canis antarticus -#> 7655954 6145382 -#> Canis dingo Canis etruscus -#> 6145383 7655938 -#> Canis mesomelas Canis lupus -#> 666235 247341 -#> Elephas armeniacus Elephas namadicus -#> 7654243 7654244 -#> Elephas zulu Elephas bombifrons -#> 7654245 3607197 -#> Elephas celebensis Palaeoloxodon lomolinoi -#> 6144032 7654246 -#> Elephas maximus -#> 541928 -#> -#> $phy -#> [1] NA -#> -#> attr(,"class") -#> [1] "datelifeQuery"+make_datelife_query2(input = c("Canis", "Elephas"), + get_spp_from_taxon = TRUE, + reference_taxonomy = "ott") +#> ---> Phylo-processing 'input'. +#> * 'input' is not a phylogeny. +#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). +#> | | | 0% | |=================================== | 50% | |======================================================================| 100% +#> ---> Getting species for the following taxon names :Canis, Elephas. +#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. +#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. +#> * There are 21 subspecies. +#> * There are 42 total species. +#> * There are 36 species in OpenTree's synthetic tree. +#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. +#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. +#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. +#> * There are 5 subspecies. +#> * There are 8 total species. +#> * There are 7 species in OpenTree's synthetic tree. +#> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree. +#> $cleaned_names +#> [1] "Canis" "Elephas" +#> +#> $tnrs_names +#> 3612500 5835572 +#> "Canis dirus" "Canis anthus" +#> 113383 752755 +#> "Canis rufus" "Canis simensis" +#> 621168 621176 +#> "Canis aureus" "Canis adustus" +#> 247331 346723 +#> "Canis latrans" "Canis himalayensis" +#> 346728 4941918 +#> "Canis indica" "Canis environmental sample" +#> 7655930 7655947 +#> "Canis ameghinoi" "Canis nehringi" +#> 7655949 7655942 +#> "Canis palustris" "Canis lanka" +#> 7655948 7655939 +#> "Canis pallipes" "Canis gezi" +#> 7655951 7655935 +#> "Canis primaevus" "Canis chrysurus" +#> 7655937 7655941 +#> "Canis dukhunensis" "Canis kokree" +#> 7655952 7655940 +#> "Canis sladeni" "Canis himalaicus" +#> 7655934 7655936 +#> "Canis chanco" "Canis curvipalatus" +#> 7655943 7655931 +#> "Canis lateralis" "Canis argentinus" +#> 7655953 7655946 +#> "Canis tarijensis" "Canis naria" +#> 7655950 7655933 +#> "Canis peruanus" "Canis cautleyi" +#> 7655954 6145382 +#> "Canis ursinus" "Canis antarticus" +#> 6145383 7655938 +#> "Canis dingo" "Canis etruscus" +#> 666235 247341 +#> "Canis mesomelas" "Canis lupus" +#> 7654243 7654244 +#> "Elephas armeniacus" "Elephas namadicus" +#> 7654245 3607197 +#> "Elephas zulu" "Elephas bombifrons" +#> 6144032 7654246 +#> "Elephas celebensis" "Palaeoloxodon lomolinoi" +#> 541928 +#> "Elephas maximus" +#> +#> $ott_ids +#> Canis dirus Canis anthus +#> 3612500 5835572 +#> Canis rufus Canis simensis +#> 113383 752755 +#> Canis aureus Canis adustus +#> 621168 621176 +#> Canis latrans Canis himalayensis +#> 247331 346723 +#> Canis indica Canis environmental sample +#> 346728 4941918 +#> Canis ameghinoi Canis nehringi +#> 7655930 7655947 +#> Canis palustris Canis lanka +#> 7655949 7655942 +#> Canis pallipes Canis gezi +#> 7655948 7655939 +#> Canis primaevus Canis chrysurus +#> 7655951 7655935 +#> Canis dukhunensis Canis kokree +#> 7655937 7655941 +#> Canis sladeni Canis himalaicus +#> 7655952 7655940 +#> Canis chanco Canis curvipalatus +#> 7655934 7655936 +#> Canis lateralis Canis argentinus +#> 7655943 7655931 +#> Canis tarijensis Canis naria +#> 7655953 7655946 +#> Canis peruanus Canis cautleyi +#> 7655950 7655933 +#> Canis ursinus Canis antarticus +#> 7655954 6145382 +#> Canis dingo Canis etruscus +#> 6145383 7655938 +#> Canis mesomelas Canis lupus +#> 666235 247341 +#> Elephas armeniacus Elephas namadicus +#> 7654243 7654244 +#> Elephas zulu Elephas bombifrons +#> 7654245 3607197 +#> Elephas celebensis Palaeoloxodon lomolinoi +#> 6144032 7654246 +#> Elephas maximus +#> 541928 +#> +#> $phy +#> [1] NA +#> +#> attr(,"class") +#> [1] "datelifeQuery"Sometimes, only some input taxon names are inclusive:
-+make_datelife_query2(input = c("Mus", "Mus musculus"), - get_spp_from_taxon = c(TRUE, FALSE), - reference_taxonomy = "ott") -#> ---> Phylo-processing 'input'. -#> * 'input' is not a phylogeny. -#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). -#> - | - | | 0% - | - |=================================== | 50% - | - |======================================================================| 100% -#> ---> Getting species for the following taxon names :Mus. -#> ---> Obtaining taxonomic data from lineages within genus 'Mus' with OTT id number = 1068778. -#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. -#> * There are 20 subspecies. -#> * There are 84 total species. -#> * There are 60 species in OpenTree's synthetic tree. -#> ---> Retrieving taxonomic info for 60 species names within 'Mus' that are in the OpenTree synthetic tree. -#> ---> Adding species data from inclusive taxon names. -#> $cleaned_names -#> [1] "Mus musculus" "Mus" -#> -#> $tnrs_names -#> -#> "Mus musculus" -#> 7067432 -#> "Mus cf. callewaerti" -#> 5857433 -#> "Mus cf. setulosus West" -#> 5857432 -#> "Mus cf. tenellus TA-2014" -#> 5857436 -#> "Mus cf. baoulei West" -#> 5857434 -#> "Mus cf. callewaerti TA-2014" -#> 3608901 -#> "Mus neavei" -#> 844274 -#> "Mus sorella" -#> 844277 -#> "Mus tenellus" -#> 844280 -#> "Mus cf. musculoides" -#> 844282 -#> "Mus bufo" -#> 3608883 -#> "Mus callewaerti" -#> 5857435 -#> "Mus mahomet" -#> 7067433 -#> "Mus sp. musculoides-minutoides DPL-2017" -#> 369735 -#> "Mus baoulei" -#> 403204 -#> "Mus emesi" -#> 996648 -#> "Mus musculoides" -#> 1000695 -#> "Mus indutus" -#> 759679 -#> "Mus mattheyi" -#> 845966 -#> "Mus minutoides" -#> 845980 -#> "Mus setulosus" -#> 1000702 -#> "Mus haussa" -#> 1000700 -#> "Mus cf. saxicola" -#> 887682 -#> "Mus shortridgei" -#> 542525 -#> "Mus saxicola" -#> 845970 -#> "Mus platythrix" -#> 348560 -#> "Mus terricolor" -#> 451263 -#> "Mus booduga" -#> 289304 -#> "Mus triton" -#> 542521 -#> "Mus spretus" -#> 542528 -#> "Mus cookii" -#> 845976 -#> "Mus spicilegus" -#> 1027340 -#> "Mus famulus" -#> 922493 -#> "Mus caroli" -#> 1010350 -#> "Mus fragilicauda" -#> 185328 -#> "Mus crociduroides" -#> 542493 -#> "Mus pahari" -#> 6144910 -#> "Mus terraereginae" -#> 7654766 -#> "Mus aegaeus" -#> 7654768 -#> "Mus camini" -#> 7654773 -#> "Mus paulina" -#> 7654776 -#> "Mus vulpinus" -#> 7654767 -#> "Mus arboricola" -#> 7654772 -#> "Mus nigrita" -#> 7654775 -#> "Mus tomentosus" -#> 7654774 -#> "Mus proconodon" -#> 7654771 -#> "Mus microdontoides" -#> 7654770 -#> "Mus leptosoma" -#> 3608899 -#> "Mus oubanguii" -#> 3608881 -#> "Mus goundae" -#> 3608904 -#> "Mus orangiae" -#> 3608880 -#> "Mus phillipsi" -#> 3608890 -#> "Mus setzeri" -#> 3608886 -#> "Mus fernandoni" -#> 3608885 -#> "Mus vulcani" -#> 3608874 -#> "Mus mayori" -#> 7654769 -#> "Mus colletti" -#> 6144906 -#> "Mus canguru" -#> 542509 -#> "Mus musculus" -#> 542519 -#> "Mus cervicolor" -#> 845973 -#> "Mus macedonicus" -#> -#> $ott_ids -#> Mus cf. callewaerti -#> 542509 7067432 -#> Mus cf. setulosus West Mus cf. tenellus TA-2014 -#> 5857433 5857432 -#> Mus cf. baoulei West Mus cf. callewaerti TA-2014 -#> 5857436 5857434 -#> Mus neavei Mus sorella -#> 3608901 844274 -#> Mus tenellus Mus cf. musculoides -#> 844277 844280 -#> Mus bufo Mus callewaerti -#> 844282 3608883 -#> Mus mahomet Mus sp. musculoides-minutoides DPL-2017 -#> 5857435 7067433 -#> Mus baoulei Mus emesi -#> 369735 403204 -#> Mus musculoides Mus indutus -#> 996648 1000695 -#> Mus mattheyi Mus minutoides -#> 759679 845966 -#> Mus setulosus Mus haussa -#> 845980 1000702 -#> Mus cf. saxicola Mus shortridgei -#> 1000700 887682 -#> Mus saxicola Mus platythrix -#> 542525 845970 -#> Mus terricolor Mus booduga -#> 348560 451263 -#> Mus triton Mus spretus -#> 289304 542521 -#> Mus cookii Mus spicilegus -#> 542528 845976 -#> Mus famulus Mus caroli -#> 1027340 922493 -#> Mus fragilicauda Mus crociduroides -#> 1010350 185328 -#> Mus pahari Mus terraereginae -#> 542493 6144910 -#> Mus aegaeus Mus camini -#> 7654766 7654768 -#> Mus paulina Mus vulpinus -#> 7654773 7654776 -#> Mus arboricola Mus nigrita -#> 7654767 7654772 -#> Mus tomentosus Mus proconodon -#> 7654775 7654774 -#> Mus microdontoides Mus leptosoma -#> 7654771 7654770 -#> Mus oubanguii Mus goundae -#> 3608899 3608881 -#> Mus orangiae Mus phillipsi -#> 3608904 3608880 -#> Mus setzeri Mus fernandoni -#> 3608890 3608886 -#> Mus vulcani Mus mayori -#> 3608885 3608874 -#> Mus colletti Mus canguru -#> 7654769 6144906 -#> Mus musculus Mus cervicolor -#> 542509 542519 -#> Mus macedonicus -#> 845973 -#> -#> $phy -#> [1] NA -#> -#> attr(,"class") -#> [1] "datelifeQuery"+make_datelife_query2(input = c("Mus", "Mus musculus"), + get_spp_from_taxon = c(TRUE, FALSE), + reference_taxonomy = "ott") +#> ---> Phylo-processing 'input'. +#> * 'input' is not a phylogeny. +#> ---> Runnning TNRS to match input names to reference taxonomy (OTT). +#> | | | 0% | |=================================== | 50% | |======================================================================| 100% +#> ---> Getting species for the following taxon names :Mus. +#> ---> Obtaining taxonomic data from lineages within genus 'Mus' with OTT id number = 1068778. +#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. +#> * There are 20 subspecies. +#> * There are 84 total species. +#> * There are 60 species in OpenTree's synthetic tree. +#> ---> Retrieving taxonomic info for 60 species names within 'Mus' that are in the OpenTree synthetic tree. +#> ---> Adding species data from inclusive taxon names. +#> $cleaned_names +#> [1] "Mus musculus" "Mus" +#> +#> $tnrs_names +#> +#> "Mus musculus" +#> 7067432 +#> "Mus cf. callewaerti" +#> 5857433 +#> "Mus cf. setulosus West" +#> 5857432 +#> "Mus cf. tenellus TA-2014" +#> 5857436 +#> "Mus cf. baoulei West" +#> 5857434 +#> "Mus cf. callewaerti TA-2014" +#> 3608901 +#> "Mus neavei" +#> 844274 +#> "Mus sorella" +#> 844277 +#> "Mus tenellus" +#> 844280 +#> "Mus cf. musculoides" +#> 844282 +#> "Mus bufo" +#> 3608883 +#> "Mus callewaerti" +#> 5857435 +#> "Mus mahomet" +#> 7067433 +#> "Mus sp. musculoides-minutoides DPL-2017" +#> 369735 +#> "Mus baoulei" +#> 403204 +#> "Mus emesi" +#> 996648 +#> "Mus musculoides" +#> 1000695 +#> "Mus indutus" +#> 759679 +#> "Mus mattheyi" +#> 845966 +#> "Mus minutoides" +#> 845980 +#> "Mus setulosus" +#> 1000702 +#> "Mus haussa" +#> 1000700 +#> "Mus cf. saxicola" +#> 887682 +#> "Mus shortridgei" +#> 542525 +#> "Mus saxicola" +#> 845970 +#> "Mus platythrix" +#> 348560 +#> "Mus terricolor" +#> 451263 +#> "Mus booduga" +#> 289304 +#> "Mus triton" +#> 542521 +#> "Mus spretus" +#> 542528 +#> "Mus cookii" +#> 845976 +#> "Mus spicilegus" +#> 1027340 +#> "Mus famulus" +#> 922493 +#> "Mus caroli" +#> 1010350 +#> "Mus fragilicauda" +#> 185328 +#> "Mus crociduroides" +#> 542493 +#> "Mus pahari" +#> 6144910 +#> "Mus terraereginae" +#> 7654766 +#> "Mus aegaeus" +#> 7654768 +#> "Mus camini" +#> 7654773 +#> "Mus paulina" +#> 7654776 +#> "Mus vulpinus" +#> 7654767 +#> "Mus arboricola" +#> 7654772 +#> "Mus nigrita" +#> 7654775 +#> "Mus tomentosus" +#> 7654774 +#> "Mus proconodon" +#> 7654771 +#> "Mus microdontoides" +#> 7654770 +#> "Mus leptosoma" +#> 3608899 +#> "Mus oubanguii" +#> 3608881 +#> "Mus goundae" +#> 3608904 +#> "Mus orangiae" +#> 3608880 +#> "Mus phillipsi" +#> 3608890 +#> "Mus setzeri" +#> 3608886 +#> "Mus fernandoni" +#> 3608885 +#> "Mus vulcani" +#> 3608874 +#> "Mus mayori" +#> 7654769 +#> "Mus colletti" +#> 6144906 +#> "Mus canguru" +#> 542509 +#> "Mus musculus" +#> 542519 +#> "Mus cervicolor" +#> 845973 +#> "Mus macedonicus" +#> +#> $ott_ids +#> Mus cf. callewaerti +#> 542509 7067432 +#> Mus cf. setulosus West Mus cf. tenellus TA-2014 +#> 5857433 5857432 +#> Mus cf. baoulei West Mus cf. callewaerti TA-2014 +#> 5857436 5857434 +#> Mus neavei Mus sorella +#> 3608901 844274 +#> Mus tenellus Mus cf. musculoides +#> 844277 844280 +#> Mus bufo Mus callewaerti +#> 844282 3608883 +#> Mus mahomet Mus sp. musculoides-minutoides DPL-2017 +#> 5857435 7067433 +#> Mus baoulei Mus emesi +#> 369735 403204 +#> Mus musculoides Mus indutus +#> 996648 1000695 +#> Mus mattheyi Mus minutoides +#> 759679 845966 +#> Mus setulosus Mus haussa +#> 845980 1000702 +#> Mus cf. saxicola Mus shortridgei +#> 1000700 887682 +#> Mus saxicola Mus platythrix +#> 542525 845970 +#> Mus terricolor Mus booduga +#> 348560 451263 +#> Mus triton Mus spretus +#> 289304 542521 +#> Mus cookii Mus spicilegus +#> 542528 845976 +#> Mus famulus Mus caroli +#> 1027340 922493 +#> Mus fragilicauda Mus crociduroides +#> 1010350 185328 +#> Mus pahari Mus terraereginae +#> 542493 6144910 +#> Mus aegaeus Mus camini +#> 7654766 7654768 +#> Mus paulina Mus vulpinus +#> 7654773 7654776 +#> Mus arboricola Mus nigrita +#> 7654767 7654772 +#> Mus tomentosus Mus proconodon +#> 7654775 7654774 +#> Mus microdontoides Mus leptosoma +#> 7654771 7654770 +#> Mus oubanguii Mus goundae +#> 3608899 3608881 +#> Mus orangiae Mus phillipsi +#> 3608904 3608880 +#> Mus setzeri Mus fernandoni +#> 3608890 3608886 +#> Mus vulcani Mus mayori +#> 3608885 3608874 +#> Mus colletti Mus canguru +#> 7654769 6144906 +#> Mus musculus Mus cervicolor +#> 542509 542519 +#> Mus macedonicus +#> 845973 +#> +#> $phy +#> [1] NA +#> +#> attr(,"class") +#> [1] "datelifeQuery"
get_opentree_species()
diff --git a/docs/deps/bootstrap-5.3.1/bootstrap.min.css b/docs/deps/bootstrap-5.3.1/bootstrap.min.css
index 984af94..4dfa488 100644
--- a/docs/deps/bootstrap-5.3.1/bootstrap.min.css
+++ b/docs/deps/bootstrap-5.3.1/bootstrap.min.css
@@ -2,4 +2,4 @@
* Bootstrap v5.3.1 (https://getbootstrap.com/)
* Copyright 2011-2023 The Bootstrap Authors
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
- */:root,[data-bs-theme="light"]{--bs-blue: #007bff;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #e83e8c;--bs-red: #ff7851;--bs-orange: #fd7e14;--bs-yellow: #ffce67;--bs-green: #56cc9d;--bs-teal: #20c997;--bs-cyan: #6cc3d5;--bs-black: #000;--bs-white: #fff;--bs-gray: #888;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #f7f7f9;--bs-gray-300: #eceeef;--bs-gray-400: #ced4da;--bs-gray-500: #aaa;--bs-gray-600: #888;--bs-gray-700: #5a5a5a;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #f3969a;--bs-primary: #78c2ad;--bs-secondary: #f3969a;--bs-success: #56cc9d;--bs-info: #6cc3d5;--bs-warning: #ffce67;--bs-danger: #ff7851;--bs-light: #f8f9fa;--bs-dark: #343a40;--bs-default-rgb: 243,150,154;--bs-primary-rgb: 120,194,173;--bs-secondary-rgb: 243,150,154;--bs-success-rgb: 86,204,157;--bs-info-rgb: 108,195,213;--bs-warning-rgb: 255,206,103;--bs-danger-rgb: 255,120,81;--bs-light-rgb: 248,249,250;--bs-dark-rgb: 52,58,64;--bs-primary-text-emphasis: 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;--bs-dropdown-link-color: #eceeef;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #78c2ad;--bs-dropdown-link-disabled-color: #aaa;--bs-dropdown-header-color: #aaa}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 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-1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) 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var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * 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.show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2890,90,90,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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.navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-md .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-md .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-md .navbar-nav-scroll{overflow:visible}.navbar-expand-md .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-md .navbar-toggler{display:none}.navbar-expand-md .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-md .offcanvas .offcanvas-header{display:none}.navbar-expand-md .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out,border-radius 0.15s ease;--bs-accordion-border-color: var(--bs-border-color);--bs-accordion-border-width: var(--bs-border-width);--bs-accordion-border-radius: var(--bs-border-radius);--bs-accordion-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%235a5a5a'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23304e45'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #bce1d6;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23aedace'%3e%3cpath 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #fff;--bs-pagination-bg: #78c2ad;--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: #78c2ad;--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: #fff;--bs-pagination-hover-bg: #f3969a;--bs-pagination-hover-border-color: #f3969a;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #f3969a;--bs-pagination-active-border-color: #f3969a;--bs-pagination-disabled-color: #fff;--bs-pagination-disabled-bg: #cce8e0;--bs-pagination-disabled-border-color: #cce8e0;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #78c2ad;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #78c2ad;--bs-list-group-active-border-color: #78c2ad;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto 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var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 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.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) 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;--bs-dropdown-link-color: #eceeef;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #78c2ad;--bs-dropdown-link-disabled-color: #aaa;--bs-dropdown-header-color: #aaa}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 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-1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) 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var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * 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.show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2890,90,90,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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.navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-md .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-md .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-md .navbar-nav-scroll{overflow:visible}.navbar-expand-md .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-md .navbar-toggler{display:none}.navbar-expand-md .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-md .offcanvas .offcanvas-header{display:none}.navbar-expand-md .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out,border-radius 0.15s ease;--bs-accordion-border-color: var(--bs-border-color);--bs-accordion-border-width: var(--bs-border-width);--bs-accordion-border-radius: var(--bs-border-radius);--bs-accordion-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%235a5a5a'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23304e45'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #bce1d6;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23aedace'%3e%3cpath 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #fff;--bs-pagination-bg: #78c2ad;--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: #78c2ad;--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: #fff;--bs-pagination-hover-bg: #f3969a;--bs-pagination-hover-border-color: #f3969a;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #f3969a;--bs-pagination-active-border-color: #f3969a;--bs-pagination-disabled-color: #fff;--bs-pagination-disabled-bg: #cce8e0;--bs-pagination-disabled-border-color: #cce8e0;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #78c2ad;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #78c2ad;--bs-list-group-active-border-color: #78c2ad;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(120,194,173,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto 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var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 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.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) 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#9acd87;color:#fff}.bg-gradient-green-teal{--bslib-color-fg: #fff;--bslib-color-bg: #40cb9b;background:linear-gradient(var(--bg-gradient-deg, 140deg), #56cc9d var(--bg-gradient-start, 36%), #20c997 var(--bg-gradient-end, 180%)) #40cb9b;color:#fff}.bg-gradient-green-cyan{--bslib-color-fg: #fff;--bslib-color-bg: #5fc8b3;background:linear-gradient(var(--bg-gradient-deg, 140deg), #56cc9d var(--bg-gradient-start, 36%), #6cc3d5 var(--bg-gradient-end, 180%)) #5fc8b3;color:#fff}.bg-gradient-teal-blue{--bslib-color-fg: #fff;--bslib-color-bg: #13aac1;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #007bff var(--bg-gradient-end, 180%)) #13aac1;color:#fff}.bg-gradient-teal-indigo{--bslib-color-fg: #fff;--bslib-color-bg: #3c7fbb;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #6610f2 var(--bg-gradient-end, 180%)) #3c7fbb;color:#fff}.bg-gradient-teal-purple{--bslib-color-fg: #fff;--bslib-color-bg: #4093a8;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #6f42c1 var(--bg-gradient-end, 180%)) #4093a8;color:#fff}.bg-gradient-teal-pink{--bslib-color-fg: #fff;--bslib-color-bg: #709193;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #e83e8c var(--bg-gradient-end, 180%)) #709193;color:#fff}.bg-gradient-teal-red{--bslib-color-fg: #fff;--bslib-color-bg: #79a97b;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #ff7851 var(--bg-gradient-end, 180%)) #79a97b;color:#fff}.bg-gradient-teal-orange{--bslib-color-fg: #fff;--bslib-color-bg: #78ab63;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #fd7e14 var(--bg-gradient-end, 180%)) #78ab63;color:#fff}.bg-gradient-teal-yellow{--bslib-color-fg: #fff;--bslib-color-bg: #79cb84;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #ffce67 var(--bg-gradient-end, 180%)) #79cb84;color:#fff}.bg-gradient-teal-green{--bslib-color-fg: #fff;--bslib-color-bg: #36ca99;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #56cc9d var(--bg-gradient-end, 180%)) #36ca99;color:#fff}.bg-gradient-teal-cyan{--bslib-color-fg: #fff;--bslib-color-bg: #3ec7b0;background:linear-gradient(var(--bg-gradient-deg, 140deg), #20c997 var(--bg-gradient-start, 36%), #6cc3d5 var(--bg-gradient-end, 180%)) #3ec7b0;color:#fff}.bg-gradient-cyan-blue{--bslib-color-fg: #fff;--bslib-color-bg: #41a6e6;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #007bff var(--bg-gradient-end, 180%)) #41a6e6;color:#fff}.bg-gradient-cyan-indigo{--bslib-color-fg: #fff;--bslib-color-bg: #6a7be1;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #6610f2 var(--bg-gradient-end, 180%)) #6a7be1;color:#fff}.bg-gradient-cyan-purple{--bslib-color-fg: #fff;--bslib-color-bg: #6d8fcd;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #6f42c1 var(--bg-gradient-end, 180%)) #6d8fcd;color:#fff}.bg-gradient-cyan-pink{--bslib-color-fg: #fff;--bslib-color-bg: #9e8eb8;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #e83e8c var(--bg-gradient-end, 180%)) #9e8eb8;color:#fff}.bg-gradient-cyan-red{--bslib-color-fg: #fff;--bslib-color-bg: #a7a5a0;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #ff7851 var(--bg-gradient-end, 180%)) #a7a5a0;color:#fff}.bg-gradient-cyan-orange{--bslib-color-fg: #fff;--bslib-color-bg: #a6a788;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #fd7e14 var(--bg-gradient-end, 180%)) #a6a788;color:#fff}.bg-gradient-cyan-yellow{--bslib-color-fg: #fff;--bslib-color-bg: #a7c7a9;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #ffce67 var(--bg-gradient-end, 180%)) #a7c7a9;color:#fff}.bg-gradient-cyan-green{--bslib-color-fg: #fff;--bslib-color-bg: #63c7bf;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #56cc9d var(--bg-gradient-end, 180%)) #63c7bf;color:#fff}.bg-gradient-cyan-teal{--bslib-color-fg: #fff;--bslib-color-bg: #4ec5bc;background:linear-gradient(var(--bg-gradient-deg, 140deg), #6cc3d5 var(--bg-gradient-start, 36%), #20c997 var(--bg-gradient-end, 180%)) #4ec5bc;color:#fff}.navbar{font-family:Montserrat,-apple-system,system-ui,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif}.btn{font-family:Montserrat,-apple-system,system-ui,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif}legend{font-family:Montserrat,-apple-system,system-ui,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica 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.row{justify-content:space-evenly}}@media (min-width: 1400px){body{font-size:18px}.col-md-3{margin-left:5rem}}.navbar-nav .nav-item>.nav-link{border-radius:.4rem;padding:0.5rem}.navbar>.container{align-items:baseline;-webkit-align-items:baseline}.navbar-light .navbar-nav .active>.nav-link{background:#f7f7f9;color:#5a5a5a}.navbar-dark .navbar-nav .active>.nav-link{background:#343a40;color:#fff}.navbar-dark .navbar-nav .nav-item>.nav-link:hover,.navbar-light .navbar-nav .nav-item>.nav-link:hover{background:rgba(120,194,173,0.1)}.navbar-dark input[type="search"]{border-color:#888;background-color:#212529;color:#f7f7f9}input[type="search"]{border-color:#eceeef;width:12rem}.headroom{will-change:transform;transition:transform 400ms ease}.headroom--pinned{transform:translateY(0%)}.headroom--unpinned{transform:translateY(-100%)}.row>main,.row>aside{margin-top:56px}html,body{scroll-padding:56px}@media (min-width: 576px){#toc{position:sticky;top:56px;max-height:calc(100vh - 56px - 1rem);overflow-y:auto}}aside h2,aside .h2{margin-top:1.5rem;font-size:1.25rem}aside .roles{color:#7b7b7b}aside .list-unstyled li{margin-bottom:0.5rem}aside .dev-status .list-unstyled li{margin-bottom:0.1rem}@media (max-width: 575.98px){aside{margin:0.5rem;width:calc(100vw - 1rem);background-color:#f8f9fa;border-color:#eceeef;border-radius:.4rem}aside h2:first-child,aside .h2:first-child{margin-top:1rem}}body{position:relative}#toc>.nav{margin-bottom:1rem}#toc>.nav a.nav-link{color:inherit;padding:0.25rem 0.5rem;margin-bottom:2px;border-radius:.4rem;border:0 solid #eceeef}#toc>.nav a.nav-link:hover,#toc>.nav a.nav-link:focus{background-color:rgba(120,194,173,0.1);color:#5a5a5a}#toc>.nav a.nav-link.active{background-color:#efefef;color:#5a5a5a}#toc>.nav .nav a.nav-link{margin-left:0.5rem}#toc>.nav .nav{display:none !important}#toc>.nav a.active+.nav{display:flex !important}footer{margin:1rem 0 1rem 0;font-size:.875em;border-top:1px solid #eceeef;background:rgba(0,0,0,0);color:#7b7b7b;display:flex;column-gap:1rem}@media (max-width: 575.98px){footer{flex-direction:column}}@media (min-width: 576px){footer .pkgdown-footer-right{text-align:right}}footer div{flex:1 1 auto}html,body{height:100%}body>.container{min-height:100%;display:flex;flex-direction:column}body>.container .row{flex:1 0 auto}::selection{background-color:#e4f3ef}main img{max-width:100%;height:auto}main table{display:block;overflow:auto}body{font-display:fallback}.page-header{border-bottom:1px solid #eceeef;padding-bottom:0.5rem;margin-bottom:0.5rem;margin-top:1.5rem}dd{margin-left:1.5rem}summary{margin-bottom:0.5rem}details{margin-bottom:1rem}.html-widget{margin-bottom:1rem}a.anchor{display:none;margin-left:5px;width:Min(0.9em, 20px);height:Min(0.9em, 20px);background-image:url(../../link.svg);background-repeat:no-repeat;background-size:Min(0.9em, 20px) Min(0.9em, 20px);background-position:center center}h2:hover .anchor,.h2:hover .anchor,h3:hover 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#e5e5e5}.tab-content{display:flex}.tab-content>.tab-pane{display:block;visibility:hidden;margin-right:-100%;width:100%}.tab-content>.active{visibility:visible}div.csl-entry{clear:both}.hanging-indent div.csl-entry{margin-left:2em;text-indent:-2em}div.csl-left-margin{min-width:2em;float:left}div.csl-right-inline{margin-left:2em;padding-left:1em}div.csl-indent{margin-left:2em}pre,pre code{word-wrap:normal}code{overflow-wrap:break-word}.hasCopyButton{position:relative}.btn-copy-ex{position:absolute;right:5px;top:5px;visibility:hidden}.hasCopyButton:hover button.btn-copy-ex{visibility:visible}pre{padding:1rem 0.5rem}@media (max-width: 575.98px){div>div>pre{margin-left:calc(var(--bs-gutter-x) * -.5);margin-right:calc(var(--bs-gutter-x) * -.5);border-radius:0;padding-left:1rem;padding-right:1rem}.btn-copy-ex{right:calc(var(--bs-gutter-x) * -.5 + 5px)}}code a:any-link{color:inherit;text-decoration-color:#888}pre code{padding:0;background:transparent}pre code .error,pre code 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diff --git a/docs/deps/bootstrap-5.3.1/font.css b/docs/deps/bootstrap-5.3.1/font.css
index 9979364..4199530 100644
--- a/docs/deps/bootstrap-5.3.1/font.css
+++ b/docs/deps/bootstrap-5.3.1/font.css
@@ -1,21 +1,135 @@
+/* cyrillic-ext */
@font-face {
font-family: 'Montserrat';
font-style: normal;
font-weight: 400;
font-display: swap;
- src: url(fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff) format('woff');
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2) format('woff2');
+ unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
}
+/* cyrillic */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 400;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2) format('woff2');
+ unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* vietnamese */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 400;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2) format('woff2');
+ unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 400;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2) format('woff2');
+ unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 400;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wlhyw.woff2) format('woff2');
+ unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 500;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2) format('woff2');
+ unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 500;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2) format('woff2');
+ unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* vietnamese */
@font-face {
font-family: 'Montserrat';
font-style: normal;
font-weight: 500;
font-display: swap;
- src: url(fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff) format('woff');
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2) format('woff2');
+ unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 500;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2) format('woff2');
+ unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 500;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wlhyw.woff2) format('woff2');
+ unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 700;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2) format('woff2');
+ unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 700;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2) format('woff2');
+ unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* vietnamese */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 700;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2) format('woff2');
+ unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+ font-family: 'Montserrat';
+ font-style: normal;
+ font-weight: 700;
+ font-display: swap;
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2) format('woff2');
+ unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
}
+/* latin */
@font-face {
font-family: 'Montserrat';
font-style: normal;
font-weight: 700;
font-display: swap;
- src: url(fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff) format('woff');
+ src: url(fonts/JTUSjIg1_i6t8kCHKm459Wlhyw.woff2) format('woff2');
+ unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
}
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diff --git a/docs/news/index.html b/docs/news/index.html
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--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -61,6 +61,9 @@ rotl::tnrs_match_names() v3.0.14get_opentree_chronograms() that have branch lengths in Myrs, no relative time.get_taxon_summary() now manages case when datelife_result is empty; throws warning instead of criptic error.testthat suite for datelife_search() inner functions.CRAN release: 2023-06-19
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 04cd6f2..60c7412 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,7 +6,7 @@ articles: fringiliidae: fringiliidae.html make_datelife_query: make_datelife_query.html making_bold_trees: making_bold_trees.html -last_built: 2024-01-05T08:47Z +last_built: 2024-06-05T04:17Z urls: reference: http://phylotastic.org/datelife/reference article: http://phylotastic.org/datelife/articles diff --git a/docs/reference/date_with_pbdb.html b/docs/reference/date_with_pbdb.html index 1c3f018..5e94035 100644 --- a/docs/reference/date_with_pbdb.html +++ b/docs/reference/date_with_pbdb.html @@ -93,7 +93,7 @@
diff --git a/docs/reference/tree_from_taxonomy.html b/docs/reference/tree_from_taxonomy.html
index 5e0d7d1..740602d 100644
--- a/docs/reference/tree_from_taxonomy.html
+++ b/docs/reference/tree_from_taxonomy.html
@@ -97,13 +97,13 @@ | MRCA Age (MY)<\/th> | Ntax<\/th> | Citation<\/th> | Newick<\/th><\/tr> | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 101.3<\/td> | 3<\/td> | Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512<\/td> | ((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3);<\/td><\/tr> | ||||||||||||||||||||
| 96.1<\/td> | 3<\/td> | Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512<\/td> | ((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1);<\/td><\/tr> | ||||||||||||||||||||
| 110.8<\/td> | 3<\/td> | Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512<\/td> | ((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8);<\/td><\/tr> | ||||||||||||||||||||
| 320.5238235<\/td> | 4<\/td> | Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845<\/td> | ((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);<\/td><\/tr><\/table>\" #> attr(,\"datelife_result\") #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Delphinus delphis #> Elephas maximus 0.0 202.6 #> Delphinus delphis 202.6 0.0 #> Felis silvestris 202.6 177.0 #> Felis silvestris #> Elephas maximus 202.6 #> Delphinus delphis 177.0 #> Felis silvestris 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Felis silvestris #> Elephas maximus 0.0 192.2 #> Felis silvestris 192.2 0.0 #> Delphinus delphis 192.2 173.6 #> Delphinus delphis #> Elephas maximus 192.2 #> Felis silvestris 173.6 #> Delphinus delphis 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Delphinus delphis Felis silvestris #> Delphinus delphis 0.0 179.6 #> Felis silvestris 179.6 0.0 #> Elephas maximus 221.6 221.6 #> Elephas maximus #> Delphinus delphis 221.6 #> Felis silvestris 221.6 #> Elephas maximus 0.0 #> #> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845` #> Felis silvestris Delphinus delphis #> Felis silvestris 0.0000 156.7850 #> Delphinus delphis 156.7850 0.0000 #> Elephas maximus 210.0193 210.0193 #> Gallus gallus 641.0476 641.0476 #> Elephas maximus Gallus gallus #> Felis silvestris 210.0193 641.0476 #> Delphinus delphis 210.0193 641.0476 #> Elephas maximus 0.0000 641.0476 #> Gallus gallus 641.0476 0.0000 #> #> attr(,\"class\") #> [1] \"datelifeResult\" #> attr(,\"datelife_query\") #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\" data_frame <- datelife::datelife_search(input = my_datelife_query, summary_format = \"data_frame\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> Age Ntax #> 1 101.3000 3 #> 2 96.1000 3 #> 3 110.8000 3 #> 4 320.5238 4 #> Citation #> 1 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4 Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Newick #> 1 ((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3); #> 2 ((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1); #> 3 ((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8); #> 4 ((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);"},{"path":[]},{"path":"http://phylotastic.org/datelife/articles/fringiliidae.html","id":"getting-species-names-within-the-family-fringillidae","dir":"Articles","previous_headings":"","what":"1. Getting species names within the family Fringillidae","title":"Case study: the true finches","text":"DateLife searches chronogram database using species names standardized unified taxonomy constructed Open Tree Life project. working taxon names species level DateLife, first step obtain species names belonging taxon interest. get species names belonging family Fringillidae, using flag get_spp_from_taxon = TRUE function datelife::make_datelife_query(): Inspect structure output: 289 species names belonging family Fringillidae according OpenTree’s unified taxonomy. provide input tree, $phy NA.","code":"dquery <- datelife::make_datelife_query(input = \"fringillidae\", get_spp_from_taxon = TRUE) #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is not a phylogeny. #> |=========================================================| 100% #> |=========================================================| 100% #> |=========================================================| 100% #> |=========================================================| 100% #> |=========================================================| 100% #> Working with the following taxa: #> Crithagra sulphurata | Crithagra citrinelloides | Crithagra mozambica | Crithagra capistrata | Crithagra burtoni | Crithagra rufobrunnea | Crithagra flaviventris | Callacanthis burtoni | Chaunoproctus ferreorostris | Rhynchostruthus socotranus | Chlorophonia cyanea | Chlorophonia occipitalis | Chlorophonia flavirostris | Akialoa obscura | Euphonia gouldi | Euphonia plumbea | Euphonia elegantissima | Euphonia luteicapilla | Euphonia chrysopasta | Euphonia fulvicrissa | Euphonia hirundinacea | Euphonia chlorotica | Euphonia cyanocephala | Euphonia rufiventris | Euphonia minuta | Euphonia cayennensis | Euphonia xanthogaster | Euphonia violacea | Euphonia pectoralis | Euphonia musica | Euphonia anneae | Euphonia affinis | Euphonia laniirostris | Euphonia finschi | Psittirostra psittacea | Urocynchramus pylzowi | Telespiza cantans | Telespiza ultima | Palmeria dolei | Oreomystis bairdi | Loxops coccineus | Loxops mana | Loxops caeruleirostris | Himatione sanguinea | Rhodopechys sanguineus | Paroreomyza montana | Pseudonestor xanthophrys | Vestiaria coccinea | Bucanetes githagineus | Hemignathus parvus | Hemignathus wilsoni | Hemignathus virens | Hemignathus munroi | Hemignathus flavus | Hemignathus kauaiensis | Hemignathus stejnegeri | Loxioides bailleui | Eremopsaltria mongolica | Rhodospiza obsoleta | Peucedramus taeniatus | Cyanerpes caeruleus | Cyanerpes cyaneus | Cyanerpes nitidus | Cyanerpes lucidus | Fringillaria goslingi | Fringillaria striolata | Fringillaria impetuani | Fringillaria poliopleura | Fringillaria tahapisi | Hemispingus atropileus | Hemispingus verticalis | Hemispingus auricularis | Hemispingus calophrys | Hemispingus rufosuperciliaris | Hemispingus superciliaris | Hemispingus trifasciatus | Hemispingus piurae | Hemispingus xanthophthalmus | Hemispingus parodii | Hemispingus goeringi | Hemispingus melanotis | Hemispingus frontalis | Hemispingus reyi | Rowettia goughensis | Embernagra platensis | Schoeniclus rusticus | Schoeniclus aureolus | Schoeniclus elegans | Schoeniclus siemsseni | Schoeniclus spodocephala | Schoeniclus yessoensis | Tersina viridis | Orthogonys chloricterus | Buarremon apertus | Buarremon assimilis | Buarremon atricapillus | Buarremon basilicus | Buarremon virenticeps | Buarremon torquatus | Peucaea aestivalis | Peucaea cassinii | Peucaea botterii | Phaeothlypis fulvicauda | Donacospiza albifrons | Platyspiza crassirostris | Melopyrrha nigra | Carduelis citrinella | Carduelis corsicana | Carduelis carduelis | Uragus sibiricus | Melamprosops phaeosoma | Hesperiphona vespertina | Pyrrhoplectes epauletta | Haemorhous mexicanus | Haemorhous purpureus | Haemorhous cassinii | Kozlowia roborowskii | Serinus syriacus | Serinus albogularis | Serinus atrogularis | Serinus citrinipectus | Serinus citrinella | Serinus pusillus | Serinus canaria | Serinus alario | Serinus striolatus | Serinus melanochrous | Serinus whytii | Serinus mennelli | Serinus reichardi | Serinus scotops | Serinus flavivertex | Serinus totta | Serinus estherae | Serinus hypostictus | Serinus leucopygius | Serinus thibetanus | Serinus gularis | Serinus dorsostriatus | Serinus canicollis | Serinus serinus | Linaria flavirostris | Linaria cannabina | Chloris monguilloti | Chloris sinica | Chloris spinoides | Chloris ambigua | Chloris chloris | Spinus yarrellii | Spinus spinus | Spinus olivaceus | Spinus uropygialis | Spinus siemiradzkii | Spinus atriceps | Spinus dominicensis | Spinus xanthogastrus | Spinus magellanicus | Spinus pinus | Spinus notatus | Spinus tristis | Spinus spinescens | Spinus crassirostris | Spinus barbatus | Spinus atratus | Spinus lawrencei | Spinus psaltria | Spinus cucullatus | Neospiza concolor | Loxia curvirostra | Loxia pytyopsittacus | Loxia leucoptera | Loxia scotica | Eophona migratoria | Eophona personata | Haematospiza sipahi | Mycerobas icterioides | Mycerobas melanozanthos | Mycerobas affinis | Mycerobas carnipes | Pinicola subhimachala | Pinicola enucleator | Linurgus olivaceus | Leucosticte sillemi | Leucosticte arctoa | Leucosticte australis | Leucosticte nemoricola | Leucosticte tephrocotis | Leucosticte atrata | Leucosticte brandti | Carpodacus vinaceus | Carpodacus rodopeplus | Carpodacus davidianus | Carpodacus rhodochlamys | Carpodacus rubescens | Carpodacus synoicus | Carpodacus severtzovi | Carpodacus rodochroa | Carpodacus erythrinus | Carpodacus roseus | Carpodacus nipalensis | Carpodacus trifasciatus | Carpodacus rubicilloides | Carpodacus pulcherrimus | Carpodacus thura | Carpodacus eos | Carpodacus rubicilla | Carpodacus grandis | Carpodacus edwardsii | Carpodacus puniceus | Carpodacus formosanus | Coccothraustes coccothraustes | Acanthis hornemanni | Acanthis cabaret | Acanthis flammea | Pyrrhula nipalensis | Pyrrhula erythaca | Pyrrhula erythrocephala | Pyrrhula murina | Pyrrhula leucogenis | Pyrrhula aurantiaca | Pyrrhula pyrrhula | Fringilla montifringilla | Fringilla teydea | Fringilla coelebs | Fringilla polatzeki | Calcarius lapponicus | Calcarius pictus | Calcarius ornatus | Calcarius mccownii | Emberiza variabilis | Emberiza hortulana | Emberiza pusilla | Emberiza cioides | Emberiza tristrami | Emberiza cabanisi | Emberiza jankowskii | Emberiza cineracea | Emberiza rutila | Emberiza sahari | Emberiza buchanani | Emberiza chrysophrys | Emberiza capensis | Emberiza cia | Emberiza schoeniclus | Emberiza stewarti | Emberiza godlewskii | Emberiza pallasi | Emberiza leucocephalos | Emberiza socotrana | Emberiza melanocephala | Emberiza bruniceps | Emberiza koslowi | Emberiza cirlus | Emberiza flaviventris | Emberiza affinis | Emberiza fucata | Emberiza citrinella | Emberiza sulphurata | Emberiza caesia | Plectrophenax nivalis | Plectrophenax hyperboreus | Melophus lathami | Cyanoloxia glaucocaerulea | Cyanoloxia cyanoides | Cyanoloxia rothschildii | Caryothraustes canadensis | Caryothraustes poliogaster | Cyanocompsa brissonii | Cyanocompsa parellina | Passerina caerulea | Passerina cyanea | Passerina amoena | Passerina ciris | Passerina leclancherii | Passerina rositae | Passerina versicolor | Parkerthraustes humeralis | Spiza americana | Pheucticus aureoventris | Pheucticus ludovicianus | Pheucticus melanocephalus | Pheucticus chrysogaster | Pheucticus tibialis | Cardinalis cardinalis | Cardinalis sinuatus | Cardinalis phoeniceus | Porphyrospiza caerulescens | Rhodothraupis celaeno | Periporphyrus erythromelas #> DateLife query done! str(dquery) #> List of 3 #> $ cleaned_names: Named chr [1:289] \"Crithagra sulphurata\" \"Crithagra #> citrinelloides\" \"Crithagra mozambica\" \"Crithagra capistrata\" ... #> ..- attr(*, \"names\")= chr [1:289] \"Fringillidae1\" \"Fringillidae2\" #> \"Fringillidae3\" \"Fringillidae4\" ... #> $ ott_ids : Named int [1:289] 903281 328908 1083721 901359 318589 #> 455546 903271 405220 242220 455541 ... #> ..- attr(*, \"names\")= chr [1:289] \"Crithagra sulphurata\" \"Crithagra #> citrinelloides\" \"Crithagra mozambica\" \"Crithagra capistrata\" ... #> $ phy : logi NA #> - attr(*, \"class\")= chr \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/fringiliidae.html","id":"search-the-species-names-across-a-chronogram-database","dir":"Articles","previous_headings":"","what":"2. Search the species names across a chronogram database","title":"Case study: the true finches","text":"Load prebuilt OpenTree chronogram database object names opentree_chronograms: Use datelifeQuery object named dquery search chronogram database: Results chronogram search returned datelifeResult object, named list patristic matrices. element list corresponds chronogram translated distance matrix patristic matrix. main reason pruning much faster matrix phylo object: Names datelifeResult object correspond study citations source chronograms:","code":"utils::data(\"opentree_chronograms\", package = \"datelife\") dres <- datelife::get_datelife_result(input = dquery, cache = opentree_chronograms) #> ... Searching the chronogram database. #> Search done! #> #> Input taxon names were found in 19 chronograms. class(dres) #> [1] \"datelifeResult\" typeof(dres) #> [1] \"list\" class(dres[[1]]) #> [1] \"matrix\" \"array\" names(dres) #> [1] \"Hooper, Daniel M., Trevor D. Price. 2017. Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecology & Evolution 1 (10): 1526-1534\" #> [2] \"Roquet, C., Lavergne, S., & Thuiller, W. (2014). One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda. PLoS Currents. doi:10.1371/currents.tol.5102670fff8aa5c918e78f5592790e48\\n\" #> [3] \"Roquet, C., Lavergne, S., & Thuiller, W. (2014). One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda. PLoS Currents. doi:10.1371/currents.tol.5102670fff8aa5c918e78f5592790e48\\n\" #> [4] \"Oliveros, C. H., Field, D. J., Ksepka, D. T., Barker, F. K., Aleixo, A., Andersen, M. J., … Faircloth, B. C. (2019). Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences, 116(16), 7916–7925. doi:10.1073/pnas.1813206116\\n\" #> [5] \"Kimball, R. T., Oliveros, C. H., Wang, N., White, N. D., Barker, F. K., Field, D. J., … Braun, E. L. (2019). A Phylogenomic Supertree of Birds. Diversity, 11(7), 109. doi:10.3390/d11070109\\n\" #> [6] \"Kimball, R. T., Oliveros, C. H., Wang, N., White, N. D., Barker, F. K., Field, D. J., … Braun, E. L. (2019). A Phylogenomic Supertree of Birds. Diversity, 11(7), 109. doi:10.3390/d11070109\\n\" #> [7] \"Uyeda, J. C., Pennell, M. W., Miller, E. T., Maia, R., & McClain, C. R. (2017). The Evolution of Energetic Scaling across the Vertebrate Tree of Life. The American Naturalist, 190(2), 185–199. doi:10.1086/692326\\n\" #> [8] \"Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845\" #> [9] \"Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845\" #> [10] \"Claramunt, Santiago, Joel Cracraft. 2015. A new time tree reveals Earth historys imprint on the evolution of modern birds. Science Advances 1 (11): e1501005-e1501005\" #> [11] \"Gibb, Gillian C., Ryan England, Gerrit Hartig, P.A. (Trish) McLenachan, Briar L. Taylor Smith, Bennet J. McComish, Alan Cooper, David Penny. 2015. New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene. Genome Biology and Evolution 7 (11): 2983-2995.\" #> [12] \"Barker, F. Keith, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk 132 (2): 333-348.\" #> [13] \"Barker, F. Keith, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk 132 (2): 333-348.\" #> [14] \"Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491 (7424): 444-448\" #> [15] \"Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491 (7424): 444-448\" #> [16] \"Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, I. J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62 (2): 298-320.\" #> [17] \"Burns, Kevin J., Allison J. Shultz, Pascal O. Title, Nicholas A. Mason, F. Keith Barker, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75: 41-77.\" #> [18] \"Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alström, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225.\" #> [19] \"Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alström, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225.\""},{"path":"http://phylotastic.org/datelife/articles/fringiliidae.html","id":"summarizing-a-dateliferesult-object","dir":"Articles","previous_headings":"","what":"3. Summarizing a datelifeResult object","title":"Case study: the true finches","text":"want plot datelifeResult chronograms individually? want single tree summarizing source chronograms? function datelife::summary.datelifeResult() get types summaries , can access later: Now can explore different age summaries.","code":"dsumm <- summary(dres, datelife_query = dquery) #> Trying with overlap = 2 #> #> Success! #> #> ... Calculating a median summary chronogram. #> |==========================================================| 100% #> |==========================================================| 100% #> |==========================================================| 100% #> 1 out of 13 chronograms tried: Ok. #> 2 out of 13 chronograms tried: Ok. #> 3 out of 13 chronograms tried: Ok. #> 4 out of 13 chronograms tried: Ok. #> 5 out of 13 chronograms tried: Ok. #> 6 out of 13 chronograms tried: Ok. #> 7 out of 13 chronograms tried: Ok. #> 8 out of 13 chronograms tried: Ok. #> 9 out of 13 chronograms tried: Ok. #> 10 out of 13 chronograms tried: Ok. #> 12 out of 19 chronograms tried: Ok. #> 13 out of 19 chronograms tried: Ok. #> 14 out of 19 chronograms tried: Ok. #> 15 out of 19 chronograms tried: Ok. #> 16 out of 19 chronograms tried: Ok. #> 17 out of 19 chronograms tried: Ok. #> 18 out of 19 chronograms tried: Failed. #> 19 out of 19 chronograms tried: Ok. #> #> Synthesizing 18 chronograms with SDM #> |==========================================================| 100% #> |==========================================================| 100% #> |==========================================================| 100%"},{"path":"http://phylotastic.org/datelife/articles/fringiliidae.html","id":"source-chronograms","dir":"Articles","previous_headings":"3. Summarizing a datelifeResult object","what":"3.1 Source chronograms:","title":"Case study: the true finches","text":"Chronograms matched database search, pruned contain species names looked called source chronograms. can accessed follow: study name: , index position:","code":"dsumm$phylo_all #> 19 phylogenetic trees dsumm$phylo_all$`Gibb, Gillian C., Ryan England, Gerrit Hartig, P.A. (Trish) McLenachan, Briar L. Taylor Smith, Bennet J. McComish, Alan Cooper, David Penny. 2015. New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene. Genome Biology and Evolution 7 (11): 2983-2995.` #> Phylogenetic tree with 7 tips and 6 internal nodes. #> #> Tip labels: #> Schoeniclus_spodocephala, Emberiza_tristrami, Emberiza_chrysophrys, #> Emberiza_pusilla, Schoeniclus_aureolus, Serinus_canaria, ... #> #> Rooted; includes branch lengths. names(dsumm$phylo_all)[1] #> [1] \"Hooper, Daniel M., Trevor D. Price. 2017. Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecology & Evolution 1 (10): 1526-1534\" dsumm$phylo_all[[1]] #> Phylogenetic tree with 44 tips and 43 internal nodes. #> #> Tip labels: #> Peucedramus_taeniatus, Peucaea_botterii, Schoeniclus_spodocephala, #> Schoeniclus_aureolus, Emberiza_chrysophrys, Emberiza_pusilla, ... #> #> Rooted; includes branch lengths."},{"path":[]},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"when-input-is-list-or-vector-of-taxon-names","dir":"Articles","previous_headings":"","what":"When input is list or vector of taxon names","title":"Making a DateLife query","text":"can process single taxon: several taxon names: case, output list:","code":"query1 <- make_datelife_query(input = \"Canis\") #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Making a DateLife query. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> ---> Working with the following taxon: Canis. #> DateLife query made! query10 <- make_datelife_query(input = rep(\"Canis\", 10)) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Making a DateLife query. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> ---> Working with the following 10 taxa: Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis. #> DateLife query made! query10 #> $cleaned_names #> [1] \"Canis\" \"Canis\" \"Canis\" \"Canis\" \"Canis\" \"Canis\" \"Canis\" \"Canis\" \"Canis\" #> [10] \"Canis\" #> #> $ott_ids #> Canis Canis Canis Canis Canis Canis Canis Canis Canis Canis #> 372706 372706 372706 372706 372706 372706 372706 372706 372706 372706 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"when-input-names-are-not-found-in-the-taxonomy","dir":"Articles","previous_headings":"","what":"When input names are not found in the taxonomy","title":"Making a DateLife query","text":"function returns NA taxonomic id missing name:","code":"make_datelife_query2(input = c(\"Canis\", \"werewolf\", \"jupiter\")) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================= | 33% #> Warning: werewolf are not matched #> | |=============================================== | 67% #> Warning: jupiter are not matched #> | |======================================================================| 100% #> $cleaned_names #> [1] \"Canis\" \"werewolf\" \"jupiter\" #> #> $tnrs_names #> [1] \"Canis\" NA NA #> #> $ott_ids #> [1] 372706 NA NA #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"subspecies-can-also-be-searched","dir":"Articles","previous_headings":"","what":"Subspecies can also be searched","title":"Making a DateLife query","text":"","code":"make_datelife_query2(input = \"Canis mesomelas elongae\") #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> $cleaned_names #> [1] \"Canis mesomelas elongae\" #> #> $tnrs_names #> [1] \"Canis mesomelas elongae\" #> #> $ott_ids #> [1] 576165 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" all_subspecies <- c(\"Canis mesomelas elongae\", \"Canis mesomelas elongae\") make_datelife_query2(input = all_subspecies) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> $cleaned_names #> [1] \"Canis mesomelas elongae\" \"Canis mesomelas elongae\" #> #> $tnrs_names #> [1] \"Canis mesomelas elongae\" \"Canis mesomelas elongae\" #> #> $ott_ids #> [1] 576165 576165 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" one_subspecies <- c(\"Canis mesomelas elongae\", \"Canis adustus\", \"Lycalopex fulvipes\") make_datelife_query2(input = one_subspecies) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% #> $cleaned_names #> [1] \"Canis mesomelas elongae\" \"Canis adustus\" #> [3] \"Lycalopex fulvipes\" #> #> $tnrs_names #> [1] \"Canis mesomelas elongae\" \"Canis adustus\" #> [3] \"Lycalopex fulvipes\" #> #> $ott_ids #> [1] 576165 621176 996573 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"choosing-between-homonyms","dir":"Articles","previous_headings":"","what":"Choosing between homonyms","title":"Making a DateLife query","text":"Taxonomic homonyms valid names used different biological entities. example, genus name Aotus refers monkey grass. TNRS smart enough choose taxonomic context set names, infallible. example, referring grass, TNRS chooses correct taxon id: referring monkey, TNRS still chooses grass: make sure get taxonomic id data taxon want, can specify “taxonomic context”:","code":"make_datelife_query2(input = c(\"Aotus\", \"Poa\", \"Arabidopsis\")) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% #> $cleaned_names #> [1] \"Aotus\" \"Poa\" \"Arabidopsis\" #> #> $tnrs_names #> [1] \"Aotus (genus in kingdom Archaeplastida)\" #> [2] \"Poa\" #> [3] \"Arabidopsis\" #> #> $ott_ids #> [1] 559026 985636 309275 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" make_datelife_query2(input = c(\"Aotus\", \"Insulacebus\", \"Microcebus\")) #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% #> $cleaned_names #> [1] \"Aotus\" \"Insulacebus\" \"Microcebus\" #> #> $tnrs_names #> [1] \"Aotus (genus in kingdom Archaeplastida)\" #> [2] \"Insulacebus\" #> [3] \"Microcebus\" #> #> $ott_ids #> [1] 559026 6145234 734824 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" rotl::tnrs_contexts() make_datelife_query2(input = c(\"Aotus\", \"Insulacebus\", \"Microcebus\"), context_name = \"Mammals\")"},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"making-a-query-from-an-inclusive-taxonomic-group","dir":"Articles","previous_headings":"","what":"Making a query from an inclusive taxonomic group","title":"Making a DateLife query","text":"can run one taxon name : two : Sometimes, input taxon names inclusive:","code":"make_datelife_query2(input = \"Canis\", get_spp_from_taxon = TRUE, reference_taxonomy = \"ott\") #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> ---> Getting species for the following taxon names :Canis. #> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. #> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. #> * There are 21 subspecies. #> * There are 42 total species. #> * There are 36 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. #> $cleaned_names #> [1] \"Canis\" #> #> $tnrs_names #> 3612500 5835572 #> \"Canis dirus\" \"Canis anthus\" #> 113383 752755 #> \"Canis rufus\" \"Canis simensis\" #> 621168 621176 #> \"Canis aureus\" \"Canis adustus\" #> 247331 346723 #> \"Canis latrans\" \"Canis himalayensis\" #> 346728 4941918 #> \"Canis indica\" \"Canis environmental sample\" #> 7655930 7655947 #> \"Canis ameghinoi\" \"Canis nehringi\" #> 7655949 7655942 #> \"Canis palustris\" \"Canis lanka\" #> 7655948 7655939 #> \"Canis pallipes\" \"Canis gezi\" #> 7655951 7655935 #> \"Canis primaevus\" \"Canis chrysurus\" #> 7655937 7655941 #> \"Canis dukhunensis\" \"Canis kokree\" #> 7655952 7655940 #> \"Canis sladeni\" \"Canis himalaicus\" #> 7655934 7655936 #> \"Canis chanco\" \"Canis curvipalatus\" #> 7655943 7655931 #> \"Canis lateralis\" \"Canis argentinus\" #> 7655953 7655946 #> \"Canis tarijensis\" \"Canis naria\" #> 7655950 7655933 #> \"Canis peruanus\" \"Canis cautleyi\" #> 7655954 6145382 #> \"Canis ursinus\" \"Canis antarticus\" #> 6145383 7655938 #> \"Canis dingo\" \"Canis etruscus\" #> 666235 247341 #> \"Canis mesomelas\" \"Canis lupus\" #> #> $ott_ids #> Canis dirus Canis anthus #> 3612500 5835572 #> Canis rufus Canis simensis #> 113383 752755 #> Canis aureus Canis adustus #> 621168 621176 #> Canis latrans Canis himalayensis #> 247331 346723 #> Canis indica Canis environmental sample #> 346728 4941918 #> Canis ameghinoi Canis nehringi #> 7655930 7655947 #> Canis palustris Canis lanka #> 7655949 7655942 #> Canis pallipes Canis gezi #> 7655948 7655939 #> Canis primaevus Canis chrysurus #> 7655951 7655935 #> Canis dukhunensis Canis kokree #> 7655937 7655941 #> Canis sladeni Canis himalaicus #> 7655952 7655940 #> Canis chanco Canis curvipalatus #> 7655934 7655936 #> Canis lateralis Canis argentinus #> 7655943 7655931 #> Canis tarijensis Canis naria #> 7655953 7655946 #> Canis peruanus Canis cautleyi #> 7655950 7655933 #> Canis ursinus Canis antarticus #> 7655954 6145382 #> Canis dingo Canis etruscus #> 6145383 7655938 #> Canis mesomelas Canis lupus #> 666235 247341 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" make_datelife_query2(input = c(\"Canis\", \"Elephas\"), get_spp_from_taxon = TRUE, reference_taxonomy = \"ott\") #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> ---> Getting species for the following taxon names :Canis, Elephas. #> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706. #> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. #> * There are 21 subspecies. #> * There are 42 total species. #> * There are 36 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. #> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. #> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. #> * There are 5 subspecies. #> * There are 8 total species. #> * There are 7 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree. #> $cleaned_names #> [1] \"Canis\" \"Elephas\" #> #> $tnrs_names #> 3612500 5835572 #> \"Canis dirus\" \"Canis anthus\" #> 113383 752755 #> \"Canis rufus\" \"Canis simensis\" #> 621168 621176 #> \"Canis aureus\" \"Canis adustus\" #> 247331 346723 #> \"Canis latrans\" \"Canis himalayensis\" #> 346728 4941918 #> \"Canis indica\" \"Canis environmental sample\" #> 7655930 7655947 #> \"Canis ameghinoi\" \"Canis nehringi\" #> 7655949 7655942 #> \"Canis palustris\" \"Canis lanka\" #> 7655948 7655939 #> \"Canis pallipes\" \"Canis gezi\" #> 7655951 7655935 #> \"Canis primaevus\" \"Canis chrysurus\" #> 7655937 7655941 #> \"Canis dukhunensis\" \"Canis kokree\" #> 7655952 7655940 #> \"Canis sladeni\" \"Canis himalaicus\" #> 7655934 7655936 #> \"Canis chanco\" \"Canis curvipalatus\" #> 7655943 7655931 #> \"Canis lateralis\" \"Canis argentinus\" #> 7655953 7655946 #> \"Canis tarijensis\" \"Canis naria\" #> 7655950 7655933 #> \"Canis peruanus\" \"Canis cautleyi\" #> 7655954 6145382 #> \"Canis ursinus\" \"Canis antarticus\" #> 6145383 7655938 #> \"Canis dingo\" \"Canis etruscus\" #> 666235 247341 #> \"Canis mesomelas\" \"Canis lupus\" #> 7654243 7654244 #> \"Elephas armeniacus\" \"Elephas namadicus\" #> 7654245 3607197 #> \"Elephas zulu\" \"Elephas bombifrons\" #> 6144032 7654246 #> \"Elephas celebensis\" \"Palaeoloxodon lomolinoi\" #> 541928 #> \"Elephas maximus\" #> #> $ott_ids #> Canis dirus Canis anthus #> 3612500 5835572 #> Canis rufus Canis simensis #> 113383 752755 #> Canis aureus Canis adustus #> 621168 621176 #> Canis latrans Canis himalayensis #> 247331 346723 #> Canis indica Canis environmental sample #> 346728 4941918 #> Canis ameghinoi Canis nehringi #> 7655930 7655947 #> Canis palustris Canis lanka #> 7655949 7655942 #> Canis pallipes Canis gezi #> 7655948 7655939 #> Canis primaevus Canis chrysurus #> 7655951 7655935 #> Canis dukhunensis Canis kokree #> 7655937 7655941 #> Canis sladeni Canis himalaicus #> 7655952 7655940 #> Canis chanco Canis curvipalatus #> 7655934 7655936 #> Canis lateralis Canis argentinus #> 7655943 7655931 #> Canis tarijensis Canis naria #> 7655953 7655946 #> Canis peruanus Canis cautleyi #> 7655950 7655933 #> Canis ursinus Canis antarticus #> 7655954 6145382 #> Canis dingo Canis etruscus #> 6145383 7655938 #> Canis mesomelas Canis lupus #> 666235 247341 #> Elephas armeniacus Elephas namadicus #> 7654243 7654244 #> Elephas zulu Elephas bombifrons #> 7654245 3607197 #> Elephas celebensis Palaeoloxodon lomolinoi #> 6144032 7654246 #> Elephas maximus #> 541928 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" make_datelife_query2(input = c(\"Mus\", \"Mus musculus\"), get_spp_from_taxon = c(TRUE, FALSE), reference_taxonomy = \"ott\") #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> ---> Getting species for the following taxon names :Mus. #> ---> Obtaining taxonomic data from lineages within genus 'Mus' with OTT id number = 1068778. #> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. #> * There are 20 subspecies. #> * There are 84 total species. #> * There are 60 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 60 species names within 'Mus' that are in the OpenTree synthetic tree. #> ---> Adding species data from inclusive taxon names. #> $cleaned_names #> [1] \"Mus musculus\" \"Mus\" #> #> $tnrs_names #> #> \"Mus musculus\" #> 7067432 #> \"Mus cf. callewaerti\" #> 5857433 #> \"Mus cf. setulosus West\" #> 5857432 #> \"Mus cf. tenellus TA-2014\" #> 5857436 #> \"Mus cf. baoulei West\" #> 5857434 #> \"Mus cf. callewaerti TA-2014\" #> 3608901 #> \"Mus neavei\" #> 844274 #> \"Mus sorella\" #> 844277 #> \"Mus tenellus\" #> 844280 #> \"Mus cf. musculoides\" #> 844282 #> \"Mus bufo\" #> 3608883 #> \"Mus callewaerti\" #> 5857435 #> \"Mus mahomet\" #> 7067433 #> \"Mus sp. musculoides-minutoides DPL-2017\" #> 369735 #> \"Mus baoulei\" #> 403204 #> \"Mus emesi\" #> 996648 #> \"Mus musculoides\" #> 1000695 #> \"Mus indutus\" #> 759679 #> \"Mus mattheyi\" #> 845966 #> \"Mus minutoides\" #> 845980 #> \"Mus setulosus\" #> 1000702 #> \"Mus haussa\" #> 1000700 #> \"Mus cf. saxicola\" #> 887682 #> \"Mus shortridgei\" #> 542525 #> \"Mus saxicola\" #> 845970 #> \"Mus platythrix\" #> 348560 #> \"Mus terricolor\" #> 451263 #> \"Mus booduga\" #> 289304 #> \"Mus triton\" #> 542521 #> \"Mus spretus\" #> 542528 #> \"Mus cookii\" #> 845976 #> \"Mus spicilegus\" #> 1027340 #> \"Mus famulus\" #> 922493 #> \"Mus caroli\" #> 1010350 #> \"Mus fragilicauda\" #> 185328 #> \"Mus crociduroides\" #> 542493 #> \"Mus pahari\" #> 6144910 #> \"Mus terraereginae\" #> 7654766 #> \"Mus aegaeus\" #> 7654768 #> \"Mus camini\" #> 7654773 #> \"Mus paulina\" #> 7654776 #> \"Mus vulpinus\" #> 7654767 #> \"Mus arboricola\" #> 7654772 #> \"Mus nigrita\" #> 7654775 #> \"Mus tomentosus\" #> 7654774 #> \"Mus proconodon\" #> 7654771 #> \"Mus microdontoides\" #> 7654770 #> \"Mus leptosoma\" #> 3608899 #> \"Mus oubanguii\" #> 3608881 #> \"Mus goundae\" #> 3608904 #> \"Mus orangiae\" #> 3608880 #> \"Mus phillipsi\" #> 3608890 #> \"Mus setzeri\" #> 3608886 #> \"Mus fernandoni\" #> 3608885 #> \"Mus vulcani\" #> 3608874 #> \"Mus mayori\" #> 7654769 #> \"Mus colletti\" #> 6144906 #> \"Mus canguru\" #> 542509 #> \"Mus musculus\" #> 542519 #> \"Mus cervicolor\" #> 845973 #> \"Mus macedonicus\" #> #> $ott_ids #> Mus cf. callewaerti #> 542509 7067432 #> Mus cf. setulosus West Mus cf. tenellus TA-2014 #> 5857433 5857432 #> Mus cf. baoulei West Mus cf. callewaerti TA-2014 #> 5857436 5857434 #> Mus neavei Mus sorella #> 3608901 844274 #> Mus tenellus Mus cf. musculoides #> 844277 844280 #> Mus bufo Mus callewaerti #> 844282 3608883 #> Mus mahomet Mus sp. musculoides-minutoides DPL-2017 #> 5857435 7067433 #> Mus baoulei Mus emesi #> 369735 403204 #> Mus musculoides Mus indutus #> 996648 1000695 #> Mus mattheyi Mus minutoides #> 759679 845966 #> Mus setulosus Mus haussa #> 845980 1000702 #> Mus cf. saxicola Mus shortridgei #> 1000700 887682 #> Mus saxicola Mus platythrix #> 542525 845970 #> Mus terricolor Mus booduga #> 348560 451263 #> Mus triton Mus spretus #> 289304 542521 #> Mus cookii Mus spicilegus #> 542528 845976 #> Mus famulus Mus caroli #> 1027340 922493 #> Mus fragilicauda Mus crociduroides #> 1010350 185328 #> Mus pahari Mus terraereginae #> 542493 6144910 #> Mus aegaeus Mus camini #> 7654766 7654768 #> Mus paulina Mus vulpinus #> 7654773 7654776 #> Mus arboricola Mus nigrita #> 7654767 7654772 #> Mus tomentosus Mus proconodon #> 7654775 7654774 #> Mus microdontoides Mus leptosoma #> 7654771 7654770 #> Mus oubanguii Mus goundae #> 3608899 3608881 #> Mus orangiae Mus phillipsi #> 3608904 3608880 #> Mus setzeri Mus fernandoni #> 3608890 3608886 #> Mus vulcani Mus mayori #> 3608885 3608874 #> Mus colletti Mus canguru #> 7654769 6144906 #> Mus musculus Mus cervicolor #> 542509 542519 #> Mus macedonicus #> 845973 #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/make_datelife_query.html","id":"the-function-get_opentree_species","dir":"Articles","previous_headings":"","what":"The function get_opentree_species()","title":"Making a DateLife query","text":"function get_opentree_species() works hood extract species names within given taxonomic group. fails: default, return species OpenTree’s synthetic tree: can override behaviour get species setting synth_tree_only = FALSE: know OTT id group, can use : get species multiple (one) taxon names:","code":"get_opentree_species() #> * Both 'taxon_name' and 'ott_id' arguments are missing. #> Please provide at least one - returning NA. #> [1] NA get_opentree_species(taxon_name = c(\"Canis\", \"Elephas\")) #> This function can only process one taxon name at a time. #> Please provide just one taxon name - returning NA. #> [1] NA get_opentree_species(ott_id = c(372706, 541927)) #> This function can only process one OTT id at a time. #> Please provide just one OTT id number - returning NA. #> [1] NA # TOFIX: # datelife::get_opentree_species(taxon_name = \"Canis\", ott_id = 541927) get_opentree_species(taxon_name = \"Canis\") #> ---> Obtaining taxonomic info for all children within OTT taxon, genus 'Canis' (input name = Canis), with OTT id number = 372706. #> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. #> * There are 21 subspecies. #> * There are 42 total species. #> * There are 36 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree. #> $tnrs_names #> 3612500 5835572 #> \"Canis dirus\" \"Canis anthus\" #> 113383 752755 #> \"Canis rufus\" \"Canis simensis\" #> 621168 621176 #> \"Canis aureus\" \"Canis adustus\" #> 247331 346723 #> \"Canis latrans\" \"Canis himalayensis\" #> 346728 4941918 #> \"Canis indica\" \"Canis environmental sample\" #> 7655930 7655947 #> \"Canis ameghinoi\" \"Canis nehringi\" #> 7655949 7655942 #> \"Canis palustris\" \"Canis lanka\" #> 7655948 7655939 #> \"Canis pallipes\" \"Canis gezi\" #> 7655951 7655935 #> \"Canis primaevus\" \"Canis chrysurus\" #> 7655937 7655941 #> \"Canis dukhunensis\" \"Canis kokree\" #> 7655952 7655940 #> \"Canis sladeni\" \"Canis himalaicus\" #> 7655934 7655936 #> \"Canis chanco\" \"Canis curvipalatus\" #> 7655943 7655931 #> \"Canis lateralis\" \"Canis argentinus\" #> 7655953 7655946 #> \"Canis tarijensis\" \"Canis naria\" #> 7655950 7655933 #> \"Canis peruanus\" \"Canis cautleyi\" #> 7655954 6145382 #> \"Canis ursinus\" \"Canis antarticus\" #> 6145383 7655938 #> \"Canis dingo\" \"Canis etruscus\" #> 666235 247341 #> \"Canis mesomelas\" \"Canis lupus\" #> #> $ott_ids #> Canis dirus Canis anthus #> 3612500 5835572 #> Canis rufus Canis simensis #> 113383 752755 #> Canis aureus Canis adustus #> 621168 621176 #> Canis latrans Canis himalayensis #> 247331 346723 #> Canis indica Canis environmental sample #> 346728 4941918 #> Canis ameghinoi Canis nehringi #> 7655930 7655947 #> Canis palustris Canis lanka #> 7655949 7655942 #> Canis pallipes Canis gezi #> 7655948 7655939 #> Canis primaevus Canis chrysurus #> 7655951 7655935 #> Canis dukhunensis Canis kokree #> 7655937 7655941 #> Canis sladeni Canis himalaicus #> 7655952 7655940 #> Canis chanco Canis curvipalatus #> 7655934 7655936 #> Canis lateralis Canis argentinus #> 7655943 7655931 #> Canis tarijensis Canis naria #> 7655953 7655946 #> Canis peruanus Canis cautleyi #> 7655950 7655933 #> Canis ursinus Canis antarticus #> 7655954 6145382 #> Canis dingo Canis etruscus #> 6145383 7655938 #> Canis mesomelas Canis lupus #> 666235 247341 get_opentree_species(taxon_name = \"Canis\", synth_tree_only = FALSE) #> ---> Obtaining taxonomic info for all children within OTT taxon, genus 'Canis' (input name = Canis), with OTT id number = 372706. #> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank. #> * There are 21 subspecies. #> * There are 42 total species. #> * There are 36 species in OpenTree's synthetic tree. #> ---> Returning taxonomic info for 42 species names within genus 'Canis'. #> $tnrs_names #> 3612500 5835572 #> \"Canis dirus\" \"Canis anthus\" #> 113383 752755 #> \"Canis rufus\" \"Canis simensis\" #> 621168 621176 #> \"Canis aureus\" \"Canis adustus\" #> 247331 346723 #> \"Canis latrans\" \"Canis himalayensis\" #> 346728 5925604 #> \"Canis indica\" \"Canis sp. KEB-2016\" #> 470950 5338950 #> \"Canis sp. CANInt1\" \"Canis sp. Russia/33,500\" #> 247325 5338951 #> \"Canis sp.\" \"Canis sp. Belgium/36,000\" #> 4941918 7655930 #> \"Canis environmental sample\" \"Canis ameghinoi\" #> 7655947 7655949 #> \"Canis nehringi\" \"Canis palustris\" #> 7655942 7655948 #> \"Canis lanka\" \"Canis pallipes\" #> 7655939 7655951 #> \"Canis gezi\" \"Canis primaevus\" #> 7655935 7655937 #> \"Canis chrysurus\" \"Canis dukhunensis\" #> 7655941 7655952 #> \"Canis kokree\" \"Canis sladeni\" #> 7655940 7655934 #> \"Canis himalaicus\" \"Canis chanco\" #> 7655936 7655943 #> \"Canis curvipalatus\" \"Canis lateralis\" #> 7655931 7655953 #> \"Canis argentinus\" \"Canis tarijensis\" #> 7655946 7655950 #> \"Canis naria\" \"Canis peruanus\" #> 7655933 7655954 #> \"Canis cautleyi\" \"Canis ursinus\" #> 6145382 6145383 #> \"Canis antarticus\" \"Canis dingo\" #> 7655938 3612504 #> \"Canis etruscus\" \"Canis spelaeus\" #> 666235 247341 #> \"Canis mesomelas\" \"Canis lupus\" #> #> $ott_ids #> Canis dirus Canis anthus #> 3612500 5835572 #> Canis rufus Canis simensis #> 113383 752755 #> Canis aureus Canis adustus #> 621168 621176 #> Canis latrans Canis himalayensis #> 247331 346723 #> Canis indica Canis sp. KEB-2016 #> 346728 5925604 #> Canis sp. CANInt1 Canis sp. Russia/33,500 #> 470950 5338950 #> Canis sp. Canis sp. Belgium/36,000 #> 247325 5338951 #> Canis environmental sample Canis ameghinoi #> 4941918 7655930 #> Canis nehringi Canis palustris #> 7655947 7655949 #> Canis lanka Canis pallipes #> 7655942 7655948 #> Canis gezi Canis primaevus #> 7655939 7655951 #> Canis chrysurus Canis dukhunensis #> 7655935 7655937 #> Canis kokree Canis sladeni #> 7655941 7655952 #> Canis himalaicus Canis chanco #> 7655940 7655934 #> Canis curvipalatus Canis lateralis #> 7655936 7655943 #> Canis argentinus Canis tarijensis #> 7655931 7655953 #> Canis naria Canis peruanus #> 7655946 7655950 #> Canis cautleyi Canis ursinus #> 7655933 7655954 #> Canis antarticus Canis dingo #> 6145382 6145383 #> Canis etruscus Canis spelaeus #> 7655938 3612504 #> Canis mesomelas Canis lupus #> 666235 247341 get_opentree_species(ott_id = 541927) #> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. #> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. #> * There are 5 subspecies. #> * There are 8 total species. #> * There are 7 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree. #> $tnrs_names #> 7654243 7654244 7654245 #> \"Elephas armeniacus\" \"Elephas namadicus\" \"Elephas zulu\" #> 3607197 6144032 7654246 #> \"Elephas bombifrons\" \"Elephas celebensis\" \"Palaeoloxodon lomolinoi\" #> 541928 #> \"Elephas maximus\" #> #> $ott_ids #> Elephas armeniacus Elephas namadicus Elephas zulu #> 7654243 7654244 7654245 #> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi #> 3607197 6144032 7654246 #> Elephas maximus #> 541928 get_opentree_species(ott_id = 541927, synth_tree_only = FALSE) #> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. #> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. #> * There are 5 subspecies. #> * There are 8 total species. #> * There are 7 species in OpenTree's synthetic tree. #> ---> Returning taxonomic info for 8 species names within genus 'Elephas'. #> $tnrs_names #> 7654243 7654244 7654245 #> \"Elephas armeniacus\" \"Elephas namadicus\" \"Elephas zulu\" #> 3607197 6144032 7654246 #> \"Elephas bombifrons\" \"Elephas celebensis\" \"Palaeoloxodon lomolinoi\" #> 3607200 541928 #> \"Elephas planifrons\" \"Elephas maximus\" #> #> $ott_ids #> Elephas armeniacus Elephas namadicus Elephas zulu #> 7654243 7654244 7654245 #> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi #> 3607197 6144032 7654246 #> Elephas planifrons Elephas maximus #> 3607200 541928 ott_ids <- c(541927, 100) # TODO: make a function out of the following code # then it can replace code inside datelife_query_get_spp, section # getting species species_list <- lapply(ott_ids, function(x) { datelife::get_opentree_species(ott_id = x, synth_tree_only = TRUE) }) #> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927. #> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species. #> * There are 5 subspecies. #> * There are 8 total species. #> * There are 7 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree. #> ---> Obtaining taxonomic data from lineages within species 'Schidax sp. 'squamaria'' with OTT id number = 100. #> * Found the following taxonomic ranks: species. #> * There are 0 subspecies. #> * There are 1 total species. #> * There are 1 species in OpenTree's synthetic tree. #> ---> Retrieving taxonomic info for 1 species names within 'Schidax sp. 'squamaria'' that are in the OpenTree synthetic tree. return_names <- unlist(sapply(species_list, \"[\", \"tnrs_names\")) return_ott_ids <- unlist(sapply(species_list, \"[\", \"ott_ids\")) names(return_names) <- return_ott_ids names(return_ott_ids) <- return_names list(tnrs_names = return_names, ott_ids = return_ott_ids) #> $tnrs_names #> 7654243 7654244 7654245 #> \"Elephas armeniacus\" \"Elephas namadicus\" \"Elephas zulu\" #> 3607197 6144032 7654246 #> \"Elephas bombifrons\" \"Elephas celebensis\" \"Palaeoloxodon lomolinoi\" #> 541928 100 #> \"Elephas maximus\" \"Schidax sp. 'squamaria'\" #> #> $ott_ids #> Elephas armeniacus Elephas namadicus Elephas zulu #> 7654243 7654244 7654245 #> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi #> 3607197 6144032 7654246 #> Elephas maximus Schidax sp. 'squamaria' #> 541928 100"},{"path":[]},{"path":"http://phylotastic.org/datelife/articles/making_bold_trees.html","id":"using-opentree-topology","dir":"Articles","previous_headings":"","what":"Using OpenTree topology:","title":"Estimating initial branch lengths","text":"","code":"# ape::comparePhylo(x = tree_nj, y = tree_acctran) otol_acctran <- phangorn::acctran(tree = ape::unroot(topology), data = Laurasiatherian) # get likelihood of acctran branch lengths and alignment otol_pml <- phangorn::pml(otol_acctran, data = Laurasiatherian) # optimize branch lengths otol_optim <- phangorn::optim.pml(otol_pml) #> optimize edge weights: -207130.4 --> -106097.5 #> optimize edge weights: -106097.5 --> -106096.6 #> optimize edge weights: -106096.6 --> -106096.6 data.frame(otol_acctran = ape::branching.times(otol_acctran), otol_optim_pml = ape::branching.times(otol_optim$tree)) #> otol_acctran otol_optim_pml #> ott244265 136.0 8.100226e-02 #> ott229558 -48.0 6.705178e-02 #> ott683263 -163.0 6.705177e-02 #> ott5334778 -205.0 6.345339e-02 #> ott392222 -264.5 4.802316e-02 #> mrcaott42ott29157 -317.5 4.802315e-02 #> mrcaott42ott10477 -363.0 4.802313e-02 #> mrcaott42ott38834 -426.5 3.757718e-02 #> mrcaott102ott739 -565.0 -1.873340e-02 #> mrcaott38834ott45520 -510.0 -5.291179e-02 #> ott44559 -412.5 3.042209e-02 #> ott644242 -407.0 -8.945198e+01 #> ott386195 -396.5 -1.319520e+02 #> mrcaott786ott83926 -491.0 -2.264520e+02 #> ott392223 -250.5 4.934326e-02 #> mrcaott1548ott4697 -290.0 3.508578e-02 #> mrcaott1548ott6790 -325.0 2.671321e-02 #> mrcaott1548ott3021 -353.0 1.838742e-02 #> ott622916 -411.0 5.608031e-03 #> mrcaott1548ott21987 -457.0 -1.454455e-03 #> mrcaott1548ott5256 -511.0 -1.051769e-02 #> ott768677 -589.0 -4.083177e-02 #> ott7655791 -556.0 -2.006278e-02 #> mrcaott5256ott44568 -658.0 -5.017645e-02 #> mrcaott44568ott226190 -721.5 -6.958462e-02 #> ott541948 -397.0 6.043458e-03 #> ott541951 -476.5 -2.445224e-02 #> ott1034218 -458.5 -1.304954e-02 #> ott574724 -386.0 1.230833e-02 #> mrcaott6790ott6794 -462.5 -6.137077e-03 #> mrcaott10323ott61857 -508.0 -8.318380e-02 #> ott813030 -488.5 -2.606782e-02 #> mrcaott4697ott6940 -349.0 2.214181e-02 #> ott827263 -408.0 1.153504e-02 #> mrcaott22064ott95364 -486.0 -1.026178e-02 #> mrcaott22064ott6145546 -561.5 -3.342281e-02 #> mrcaott3285ott17250 -321.0 -5.802449e-02 #> mrcaott3285ott60434 -359.0 -1.005802e+01 #> mrcaott72667ott180375 -239.0 4.144542e-02 #> ott746703 -318.0 -2.134463e-03 #> mrcaott82081ott292026 -418.5 -1.005021e+02 #> ott922729 -508.5 -1.005021e+02 #> mrcaott6735ott29033 -259.0 -2.109329e+02 #> mrcaott6735ott70811 -321.0 -2.109329e+02 #> mrcaott6735ott44497 -385.0 -2.109329e+02 plot(otol_pml, main=\"ACCTRAN branches\", cex = 0.8) # top = default plot(otol_optim, main=\"optimized branches\", cex = 0.8) # bottom = optimized branch lengths"},{"path":"http://phylotastic.org/datelife/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Brian O'Meara. Author. Jonathan Eastman. Author. Tracy Heath. Author. April Wright. Author. Klaus Schliep. Author. Scott Chamberlain. Author. Peter Midford. Author. Luke Harmon. Author. Joseph Brown. Author. Matt Pennell. Author. Mike Alfaro. Author. Luna L. Sanchez Reyes. Author, maintainer. Emily Jane McTavish. Contributor.","code":""},{"path":"http://phylotastic.org/datelife/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Brian O'Meara, Luna L. Sanchez-Reyes, Jonathan Eastman, Tracy Heath, April Wright, Klaus Schliep, Scott Chamberlain, Peter Midford, Luke Harmon, Joseph Brown, Matt Pennell, Mike Alfaro, Emily Jane McTavish. 2024. datelife: Scientific Data Time Lineage Divergence Taxa. R package version 0.6.9 Luna L. Sanchez-Reyes, Emily Jane McTavish, Brian O'Meara. 2022. datelife: Leveraging databases analytical tools reveal dated Tree Life. bioRxiv 782094; doi: https://doi.org/10.1101/782094","code":"@Manual{, title = {datelife: Scientific Data on Time of Lineage Divergence for Your Taxa}, author = {Brian O'Meara and Luna L. Sanchez-Reyes and Jonathan Eastman and Tracy Heath and April Wright and Klaus Schliep and Scott Chamberlain and Peter Midford and Luke Harmon and Joseph Brown and Matt Pennell and Mike Alfaro and Emily Jane McTavish}, year = {2024}, note = {R package version 0.6.9}, url = {https://doi.org/10.5281/zenodo.593938}, } @Article{, title = {datelife: Leveraging databases and analytical tools to reveal the dated Tree of Life}, author = {Luna L. Sanchez-Reyes and Emily Jane McTavish and Brian O'Meara}, journal = {bioRxiv}, year = {2022}, volume = {782094}, url = {https://doi.org/10.1101/782094}, }"},{"path":[]},{"path":"http://phylotastic.org/datelife/index.html","id":"what-is-datelife","dir":"","previous_headings":"","what":"What is datelife?","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"datelife R package allows researchers general audience obtain open scientific data age organism interested , retrieving organism ages database dated phylogenetic trees (aka chronograms), peer-reviewed published part scientific research article, indexed journal (Open Tree Life’s tree store). , organism ages retrieved datelife constitute state---art, peer-reviewed, public scientific knowledge, can accessed reused experts non-experts field alike.","code":""},{"path":"http://phylotastic.org/datelife/index.html","id":"how-can-you-use-datelife","dir":"","previous_headings":"","what":"How can you use datelife?","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"can install datelife R package computer use locally. can find instructions local installation . want/time deal installation R code, can use DateLife’s interactive website application. Note website live moment, apologies.","code":""},{"path":"http://phylotastic.org/datelife/index.html","id":"documentation-topics","dir":"","previous_headings":"","what":"Documentation topics:","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"Local installation Getting started Case Study: true finches Making datelife query Estimating initial branch lengths Function documentation","code":""},{"path":"http://phylotastic.org/datelife/index.html","id":"local-installation-of-the-datelife-r-package","dir":"","previous_headings":"","what":"Local installation of the datelife R package","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"datelife’s recent stable version can installed : datelife’s previous stable versions available installation CRAN repository. example, install version 0.6.1, can run: can install datelife’s development version GitHub repository :","code":"install.packages(\"datelife\") devtools::install_version(\"datelife\", version=\"0.6.1\") devtools::install_github(\"phylotastic/datelife\")"},{"path":"http://phylotastic.org/datelife/index.html","id":"citing-datelife","dir":"","previous_headings":"","what":"Citing datelife","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"use datelife publication, please cite R package accompanying paper: O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright , Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M, McTavish E (2024). datelife: Scientific Data Time Lineage Divergence Taxa. R package version 0.6.9, https://doi.org/10.5281/zenodo.593938. Sanchez-Reyes L, McTavish E, O’Meara B (2022). “datelife: Leveraging databases analytical tools reveal dated Tree Life.” bioRxiv, 782094. https://doi.org/10.1101/782094. can get citations bibtex entry :","code":"citation(\"datelife\") toBibtex(citation(\"datelife\"))"},{"path":"http://phylotastic.org/datelife/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"package free open source software, licensed GPL.","code":""},{"path":"http://phylotastic.org/datelife/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"Scientific Data on Time of Lineage Divergence for Your Taxa","text":"datelife developed part phylotastic (NSF-funded) project, still development.","code":""},{"path":"http://phylotastic.org/datelife/reference/birds_and_cats.html","id":null,"dir":"Reference","previous_headings":"","what":"A multiPhylo object with trees resulting from a datelife search of some birds and cats species — birds_and_cats","title":"A multiPhylo object with trees resulting from a datelife search of some birds and cats species — birds_and_cats","text":"multiPhylo object trees resulting datelife search birds cats species","code":""},{"path":"http://phylotastic.org/datelife/reference/birds_and_cats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A multiPhylo object with trees resulting from a datelife search of some birds and cats species — birds_and_cats","text":"","code":"birds_and_cats"},{"path":"http://phylotastic.org/datelife/reference/birds_and_cats.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A multiPhylo object with trees resulting from a datelife search of some birds and cats species — birds_and_cats","text":"multiPhylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/birds_and_cats.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A multiPhylo object with trees resulting from a datelife search of some birds and cats species — birds_and_cats","text":"Generated : taxa <- c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\", \"Gallus\", \"Felis\") birds_and_cats <- datelife_search(input = taxa, summary_format = \"phylo_all\", get_spp_from_taxon = TRUE) usethis::use_data(birds_and_cats)","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Build grove list — build_grove_list","title":"Build grove list — build_grove_list","text":"function implements theorem 1.1 Ané et al. (2009) doi:10.1007/s00026-009-0017-x find grove given group chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build grove list — build_grove_list","text":"","code":"build_grove_list(datelife_result, n = 2)"},{"path":"http://phylotastic.org/datelife/reference/build_grove_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build grove list — build_grove_list","text":"datelife_result datelifeResult object. n degree taxon name overlap among input chronograms. Defaults n = 2, .e., least two overlapping taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build grove list — build_grove_list","text":"list vectors; list element grove.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","title":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","text":"function implements theorem 1.1 Ané et al. (2009) doi:10.1007/s00026-009-0017-x find grove given group chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","text":"","code":"build_grove_matrix(datelife_result, n = 2)"},{"path":"http://phylotastic.org/datelife/reference/build_grove_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","text":"datelife_result datelifeResult object. n degree taxon name overlap among input chronograms. Defaults n = 2, .e., least two overlapping taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","text":"matrix. cell shows whether n-overlap exists pair inputs.","code":""},{"path":"http://phylotastic.org/datelife/reference/build_grove_matrix.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Find the grove for a group of chronograms and build a matrix. — build_grove_matrix","text":"Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). \"Groves phylogenetic trees\". Annals Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x .","code":""},{"path":"http://phylotastic.org/datelife/reference/check_conflicting_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for conflicting calibrations. — check_conflicting_calibrations","title":"Check for conflicting calibrations. — check_conflicting_calibrations","text":"check_conflicting_calibrations checks calibrations younger older relative descendants ancestors, respectively.","code":""},{"path":"http://phylotastic.org/datelife/reference/check_conflicting_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for conflicting calibrations. — check_conflicting_calibrations","text":"","code":"check_conflicting_calibrations(phy, calibration_distribution)"},{"path":"http://phylotastic.org/datelife/reference/check_conflicting_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for conflicting calibrations. — check_conflicting_calibrations","text":"phy phylo object. calibration_distribution list node age distributions, named phy's node numbers.","code":""},{"path":"http://phylotastic.org/datelife/reference/check_conflicting_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check for conflicting calibrations. — check_conflicting_calibrations","text":"removes conflicting calibrations needed, BLADJ works long age root.","code":""},{"path":"http://phylotastic.org/datelife/reference/check_ott_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check input for usage in other datelife functions — check_ott_input","title":"Check input for usage in other datelife functions — check_ott_input","text":"check_ott_input currently used functions get_ott_clade(), get_ott_children(), get_otol_synthetic_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/check_ott_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check input for usage in other datelife functions — check_ott_input","text":"","code":"check_ott_input(input = NULL, ott_ids = NULL, ...)"},{"path":"http://phylotastic.org/datelife/reference/check_ott_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check input for usage in other datelife functions — check_ott_input","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). ... Arguments passed make_datelife_query use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\".","code":""},{"path":"http://phylotastic.org/datelife/reference/check_ott_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check input for usage in other datelife functions — check_ott_input","text":"named numeric vector valid Open Tree Taxonomy (OTT) ids.","code":""},{"path":"http://phylotastic.org/datelife/reference/check_ott_input.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check input for usage in other datelife functions — check_ott_input","text":"default, uses ott_id argument NULL.","code":""},{"path":"http://phylotastic.org/datelife/reference/choose_cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose an ultrametric phylo object from cluster_patristicmatrix() obtained\nwith a particular clustering method, or the next best tree.\nIf there are no ultrametric trees, it does not force them to be ultrametric. — choose_cluster","title":"Choose an ultrametric phylo object from cluster_patristicmatrix() obtained\nwith a particular clustering method, or the next best tree.\nIf there are no ultrametric trees, it does not force them to be ultrametric. — choose_cluster","text":"Choose ultrametric phylo object cluster_patristicmatrix() obtained particular clustering method, next best tree. ultrametric trees, force ultrametric.","code":""},{"path":"http://phylotastic.org/datelife/reference/choose_cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose an ultrametric phylo object from cluster_patristicmatrix() obtained\nwith a particular clustering method, or the next best tree.\nIf there are no ultrametric trees, it does not force them to be ultrametric. — choose_cluster","text":"","code":"choose_cluster(phycluster, clustering_method = \"nj\")"},{"path":"http://phylotastic.org/datelife/reference/choose_cluster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose an ultrametric phylo object from cluster_patristicmatrix() obtained\nwith a particular clustering method, or the next best tree.\nIf there are no ultrametric trees, it does not force them to be ultrametric. — choose_cluster","text":"phycluster output cluster_patristicmatrix() clustering_method character vector indicating method construct tree. Options : nj Neighbor-Joining method applied ape::nj(). upgma Unweighted Pair Group Method Arithmetic Mean method applied phangorn::upgma(). bionj improved version Neighbor-Joining method applied ape::bionj(). triangle Triangles method applied ape::triangMtd() mvr Minimum Variance Reduction method applied ape::mvr().","code":""},{"path":"http://phylotastic.org/datelife/reference/choose_cluster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose an ultrametric phylo object from cluster_patristicmatrix() obtained\nwith a particular clustering method, or the next best tree.\nIf there are no ultrametric trees, it does not force them to be ultrametric. — choose_cluster","text":"phylo object NA.","code":""},{"path":"http://phylotastic.org/datelife/reference/classification_paths_from_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","title":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","text":"uses taxize package's wrapper Global Names Resolver get taxonomic paths vector taxa pass . Sources vector source labels order (though works best everything uses taxonomy, recommend just one source). can see options taxize::gnr_datasources(). default Catalogue Life","code":""},{"path":"http://phylotastic.org/datelife/reference/classification_paths_from_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","text":"","code":"classification_paths_from_taxonomy(taxa, sources = \"Catalogue of Life\")"},{"path":"http://phylotastic.org/datelife/reference/classification_paths_from_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","text":"taxa Vector taxon names sources Vector names preferred sources; see taxize::gnr_datasources(). Currently supports 100 taxonomic resources, see details.","code":""},{"path":"http://phylotastic.org/datelife/reference/classification_paths_from_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","text":"list resolved taxa (tibble, taxize::gnr_resolve) vector taxa resolved","code":""},{"path":"http://phylotastic.org/datelife/reference/classification_paths_from_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Gets classification paths for a vector of taxa — classification_paths_from_taxonomy","text":"Taxonomies supported taxize::gnr_datasources() Catalogue Life Wikispecies ITIS NCBI Index Fungorum GRIN Taxonomy Plants Union 4 Interim Register Marine Nonmarine Genera World Register Marine Species Freebase GBIF Backbone Taxonomy EOL Passiflora vernacular names Inventory Fish Species Wami River Basin Pheasant Diversity Conservation Mt. Gaoligonshan Region Finding Species Birds Lindi Forests Plantation Nemertea Kihansi Gorge Amphibian Species Checklist Mushroom Observer TaxonConcept Amphibia Reptilia Yunnan Common names Chilean Plants Invasive Species Belgium ZooKeys COA Wildlife Conservation List AskNature China: Yunnan, Southern Gaoligongshan, Rapid Biological Inventories Report . 04 Native Orchids Gaoligongshan Mountains, China Illinois Wildflowers Coleorrhyncha Species File /home/dimus/files/dwca/zoological names.zip Peces de la zona hidrogeográfica de la Amazonia, Colombia (Spreadsheet) Eastern Mediterranean Syllidae Gaoligong Shan Medicinal Plants Checklist birds_of_tanzania AmphibiaWeb tanzania_plant_sepecimens Papahanaumokuakea Marine National Monument Taiwanese IUCN species list BioPedia AnAge Embioptera Species File Global Invasive Species Database Sendoya S., Fernández F. AAT de hormigas (Hymenoptera: Formicidae) del Neotrópico 1.0 2004 (Spreadsheet) Flora Gaoligong Mountains ARKive True Fruit Flies (Diptera, Tephritidae) Afrotropical Region 3i - Typhlocybinae Database CATE Sphingidae ZooBank Diatoms AntWeb Endemic species Taiwan Dermaptera Species File Mantodea Species File Birds World: Recommended English Names New Zealand Animalia Blattodea Species File Plecoptera Species File /home/dimus/files/dwca/clemens.zip Coreoidea Species File Freshwater Animal Diversity Assessment - Normalized export Catalogue Vascular Plant Species Central Northeastern Brazil Wikipedia EOL Database Vascular Plants Canada (VASCAN) Phasmida Species File OBIS USDA NRCS PLANTS Database Catalog Fishes Aphid Species File National Checklist Taiwan Psocodea Species File FishBase 3i - Typhlocybinae Database Belgian Species List EUNIS CU*STAR Orthoptera Species File Bishop Museum IUCN Red List Threatened Species BioLib.cz Tropicos - Missouri Botanical Garden nlbif International Plant Names Index Index Organism Names uBio NameBank Arctos Checklist Beetles (Coleoptera) Canada Alaska. Second Edition. Paleobiology Database Reptile Database Mammal Species World BirdLife International Checklist da Flora de Portugal (Continental, Açores e Madeira) FishBase Cache Silva Open Tree Life Reference Taxonomy iNaturalist Interim Register Marine Nonmarine Genera Gymno","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_ott_chronogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","title":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","text":"Clean issues Open Tree Life chronograms now 1) checks unmapped taxa maps tnrs_match.phylo, 2) roots chronogram unrooted","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_ott_chronogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","text":"","code":"clean_ott_chronogram(phy)"},{"path":"http://phylotastic.org/datelife/reference/clean_ott_chronogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_ott_chronogram.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","text":"object class data frame phylo, added class match_names. NULL NULL","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_ott_chronogram.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Clean up some issues with Open Tree of Life chronograms\nFor now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted — clean_ott_chronogram","text":"limit number names can queried matched. output preserve elements original input phylo object add phy$mapped character vector indicating state mapping phy$tip.labels: phy$original.tip.label character vector preserving original labels. phy$ott_ids numeric vector ott id numbers matched tips. Unmatched original tips NaN. tips duplicated, tnrs run (avoiding increases function running time) result applied duplicated tip labels","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_taxon_info_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify, extract and clean taxonomic children names from a taxonomy_taxon_info()\noutput. — clean_taxon_info_children","title":"Identify, extract and clean taxonomic children names from a taxonomy_taxon_info()\noutput. — clean_taxon_info_children","text":"clean_taxon_info_children eliminates taxa give problems trying retrieve induced subtree Open Tree Life.","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_taxon_info_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify, extract and clean taxonomic children names from a taxonomy_taxon_info()\noutput. — clean_taxon_info_children","text":"","code":"clean_taxon_info_children( taxon_info, invalid = c(\"barren\", \"extinct\", \"uncultured\", \"major_rank_conflict\", \"incertae_sedis\", \"unplaced\", \"conflict\", \"environmental\", \"not_otu\", \"hidden\", \"hybrid\") )"},{"path":"http://phylotastic.org/datelife/reference/clean_taxon_info_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify, extract and clean taxonomic children names from a taxonomy_taxon_info()\noutput. — clean_taxon_info_children","text":"taxon_info output rotl::taxonomy_taxon_info(). invalid character vector \"flags\", .e., characteristics used Open Tree Life Taxonomy detect invalid taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_taxon_info_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify, extract and clean taxonomic children names from a taxonomy_taxon_info()\noutput. — clean_taxon_info_children","text":"list valid children unique OTT names, OTT ids taxonomic ranks.","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_tnrs.html","id":null,"dir":"Reference","previous_headings":"","what":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","title":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","text":"Eliminates unmatched (NAs) invalid taxa rotl::tnrs_match_names() tnrs_match() output Useful get ott ids retrieve induced synthetic Open Tree Life. Needed using include_suppressed = FALSE rotl::tnrs_match_names() drop invalid taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_tnrs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","text":"","code":"clean_tnrs( tnrs, invalid = c(\"barren\", \"extinct\", \"uncultured\", \"major_rank_conflict\", \"incertae\", \"unplaced\", \"conflict\", \"environmental\", \"not_otu\"), remove_nonmatches = FALSE )"},{"path":"http://phylotastic.org/datelife/reference/clean_tnrs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","text":"tnrs data frame, usually output datelife::tnrs_match rotl::tnrs_match_names functions, see details. invalid character string flags removed final object. remove_nonmatches Boolean, whether remove unsuccessfully matched names .","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_tnrs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","text":"data frame named list (depending input) valid taxa .","code":""},{"path":"http://phylotastic.org/datelife/reference/clean_tnrs.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output\nUseful to get ott ids to retrieve an induced synthetic Open Tree of Life.\nNeeded because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs","text":"Input can data frame named list relates taxa stored element named \"unique\" validity category stored \"flags\".","code":""},{"path":"http://phylotastic.org/datelife/reference/cluster_patristicmatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","title":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","text":"Cluster patristic matrix tree various methods.","code":""},{"path":"http://phylotastic.org/datelife/reference/cluster_patristicmatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","text":"","code":"cluster_patristicmatrix(patristic_matrix, variance_matrix = NULL)"},{"path":"http://phylotastic.org/datelife/reference/cluster_patristicmatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","text":"patristic_matrix patristic matrix variance_matrix variance matrix datelifeResult object, usually output datelife_result_variance_matrix(). used clustering_method = \"mvr\".","code":""},{"path":"http://phylotastic.org/datelife/reference/cluster_patristicmatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","text":"list trees obtained clustering methods detailed patristic_matrix_to_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/cluster_patristicmatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cluster a patristic matrix into a tree with various methods. — cluster_patristicmatrix","text":"clustering method fails, NA returned.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify and Check. — congruify_and_check","title":"Congruify and Check. — congruify_and_check","text":"Congruify Check.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify and Check. — congruify_and_check","text":"","code":"congruify_and_check( reference, target, taxonomy = NULL, tol = 0.01, option = 2, scale = \"pathd8\", attempt_fix = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/congruify_and_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify and Check. — congruify_and_check","text":"reference ultrametric tree used time-scale target target phylogram sought ultrametricized based reference phylogeny taxonomy linkage table tips phylogeny clades represented tree; rownames 'taxonomy' tips found phylogeny tol branching time reference secondary constraints applied target option integer (1 2; see details). scale NA, \"PATHd8\" \"treePL\" (PATHd8 \"treePL\" available R PATH) attempt_fix Default TRUE. congruification results NA branch lengths, attempt fix .","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca","text":"Congruify nodes tree topology nodes source chronogram, find mrca nodes","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca","text":"","code":"congruify_and_mrca(phy)"},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca","text":"object class data frame.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca.phylo","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca.phylo","text":"congruify_and_mrca congruifies target tree single source chronogram, gets nodes target tree correspond recent common ancestor (mrca) taxon pairs congruified calibrations. uses phytools::findMRCA() get mrca nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca.phylo","text":"","code":"# S3 method for phylo congruify_and_mrca(phy, source_chronogram, study)"},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca.phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca.phylo","text":"phy phylo object. source_chronogram phylo object, output datelife_search(). study character string indicating name study source_chronogram comes .","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_multiPhylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_multiPhylo","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_multiPhylo","text":"congruify_and_mrca_multiPhylo congruifies target tree source chronograms multiPhylo object, gets nodes target tree correspond recent common ancestor (mrca) taxon pairs congruified calibrations. calls congruify_and_mrca_phylo(), phytools::findMRCA() get mrca nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_multiPhylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_multiPhylo","text":"","code":"congruify_and_mrca_multiPhylo(phy, source_chronograms)"},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_multiPhylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_multiPhylo","text":"phy phylo object. source_chronograms multiPhylo object, output datelife_search().","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_multiPhylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_multiPhylo","text":"data.frame node ages source_chronograms corresponding mrca nodes target tree phy. attributes(return)$phy stores congruified mrca matched phylogeny.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_phylo","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_phylo","text":"congruify_and_mrca congruifies target tree single source chronogram, gets nodes target tree correspond recent common ancestor (mrca) taxon pairs congruified calibrations. uses phytools::findMRCA() get mrca nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_phylo","text":"","code":"congruify_and_mrca_phylo(phy, source_chronogram, reference)"},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_phylo","text":"phy phylo object. source_chronogram phylo object, output datelife_search(). reference character string indicating study reference source_chronogram comes .","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_and_mrca_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes — congruify_and_mrca_phylo","text":"data.frame node ages source_chronograms corresponding mrca nodes target tree phy.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","title":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","text":"congruify_calibrations get nodes tree topology given phy correspond recent common ancestor (mrca) taxon pairs given calibrations. uses phytools::findMRCA() get mrca nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","text":"","code":"congruify_calibrations(phy, chronograms, calibrations)"},{"path":"http://phylotastic.org/datelife/reference/congruify_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","text":"phy phylo object. chronograms phylo multiPhylo object, output datelife_search(). calibrations calibrations object, output extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","text":"list two elements: matched_phy phylo object nodes renamed match results mrca search. Nodes renamed using tree_add_nodelabels(). matched_calibrations matchedCalibrations object, input calibrations object two additional columns storing results mrca search phytools::findMRCA(): $mrca_node_number $mrca_node_name.","code":""},{"path":"http://phylotastic.org/datelife/reference/congruify_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Congruify nodes of a tree topology to nodes from taxon pair calibrations — congruify_calibrations","text":"function takes pairs taxon names calibrations data frame, looks vector tip labels tree. present, gets node represents recent common ancestor (mrca) pair taxa tree. Nodes input phy can named . renamed.","code":""},{"path":"http://phylotastic.org/datelife/reference/contributor_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","title":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","text":"Information contributors, authors, study ids clades studies chronograms Open Tree Life (Open Tree)","code":""},{"path":"http://phylotastic.org/datelife/reference/contributor_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","text":"","code":"contributor_cache"},{"path":"http://phylotastic.org/datelife/reference/contributor_cache.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","text":"list five data sets. author.pretty character vector author names studies chronograms Open Tree. author.results dataframe three variables: authors, study ids clades. curator.pretty character vector names curators chronograms Open Tree. curator.results data.frame three variables: curators, study ids clades. missed_doi character vector study ids whose \"doi\" retrieved.","code":""},{"path":"http://phylotastic.org/datelife/reference/contributor_cache.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/contributor_cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Information on contributors, authors, study ids and clades from studies with\nchronograms in Open Tree of Life (Open Tree) — contributor_cache","text":"Generated make_contributor_cache().","code":""},{"path":"http://phylotastic.org/datelife/reference/date_with_pbdb.html","id":null,"dir":"Reference","previous_headings":"","what":"Date with Paleobiology Database and paleotree. — date_with_pbdb","title":"Date with Paleobiology Database and paleotree. — date_with_pbdb","text":"take topology, look information fossils taxa tree, use paleotree::timePaleoPhy() compute branch lengths.","code":""},{"path":"http://phylotastic.org/datelife/reference/date_with_pbdb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date with Paleobiology Database and paleotree. — date_with_pbdb","text":"","code":"date_with_pbdb(phy, recent = FALSE, assume_recent_if_missing = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/date_with_pbdb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date with Paleobiology Database and paleotree. — date_with_pbdb","text":"phy phylo object. recent TRUE, forces minimum age zero taxon assume_recent_if_missing TRUE, taxon missing PBDB assumed recent.","code":""},{"path":"http://phylotastic.org/datelife/reference/date_with_pbdb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date with Paleobiology Database and paleotree. — date_with_pbdb","text":"dated tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/date_with_pbdb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Date with Paleobiology Database and paleotree. — date_with_pbdb","text":"","code":"if (FALSE) # This is a flag for package development. You are welcome to run the example. taxa <- c( \"Archaeopteryx\", \"Pinus\", \"Quetzalcoatlus\", \"Homo sapiens\", \"Tyrannosaurus rex\", \"Megatheriidae\", \"Metasequoia\", \"Aedes\", \"Panthera\" ) phy <- tree_from_taxonomy(taxa, sources = \"The Paleobiology Database\")$phy #> Error in lapply(x, f): object 'taxa' not found # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/datelife_authors_tabulate.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the relevant authors for a set of studies. — datelife_authors_tabulate","title":"Return the relevant authors for a set of studies. — datelife_authors_tabulate","text":"Return relevant authors set studies.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_authors_tabulate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the relevant authors for a set of studies. — datelife_authors_tabulate","text":"","code":"datelife_authors_tabulate(results.index, cache = \"opentree_chronograms\")"},{"path":"http://phylotastic.org/datelife/reference/datelife_authors_tabulate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the relevant authors for a set of studies. — datelife_authors_tabulate","text":"results.index vector datelife_result_study_index() indices relevant studies. cache cached chronogram database.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_authors_tabulate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the relevant authors for a set of studies. — datelife_authors_tabulate","text":"vector counts author, names equal author names.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_MRCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result(). — datelife_result_MRCA","title":"Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result(). — datelife_result_MRCA","text":"Get numeric vector MRCAs datelifeResult object. Used summarize_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_MRCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result(). — datelife_result_MRCA","text":"","code":"datelife_result_MRCA(datelife_result, na_rm = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_MRCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result(). — datelife_result_MRCA","text":"datelife_result datelifeResult object, usually output get_datelife_result(). na_rm TRUE, drops rows containing NAs datelifeResult patristic matrix; FALSE, returns NA missing entries.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_MRCA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result(). — datelife_result_MRCA","text":"named numeric vector MRCA ages element given datelife_result.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a median summary chronogram from a datelifeResult object. — datelife_result_median","title":"Get a median summary chronogram from a datelifeResult object. — datelife_result_median","text":"Get median summary chronogram datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a median summary chronogram from a datelifeResult object. — datelife_result_median","text":"","code":"datelife_result_median(datelife_result, ...)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a median summary chronogram from a datelifeResult object. — datelife_result_median","text":"datelife_result datelifeResult object, usually output get_datelife_result(). ... Arguments passed summary_matrix_to_phylo summ_matrix summary patristic distance matrix, ones obtained datelife_result_sdm_matrix() datelife_result_median_matrix(). total_distance Whether input summ_matrix stores total age distance (tip tip) distance node tip. Default TRUE, divides matrix half, FALSE take . use character vector indicating type age use summary tree. One following: \"mean\" use mean() node ages summ_matrix. \"median\" uses stats::median() age node ages summ_matrix. \"min\" use min() age node ages summ_matrix. \"max\" Choose wanna conservative; use max() age node ages summ_matrix. \"midpoint\" use mean minimum age maximum age. target_tree phylo object. Use case want specific backbone output tree. datelife_query datelifeQuery object, usually output make_datelife_query().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a median summary chronogram from a datelifeResult object. — datelife_result_median","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute a median matrix of a datelifeResult object. — datelife_result_median_matrix","title":"Compute a median matrix of a datelifeResult object. — datelife_result_median_matrix","text":"Compute median matrix datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute a median matrix of a datelifeResult object. — datelife_result_median_matrix","text":"","code":"datelife_result_median_matrix(datelife_result)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute a median matrix of a datelifeResult object. — datelife_result_median_matrix","text":"datelife_result datelifeResult object, usually output get_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_median_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute a median matrix of a datelifeResult object. — datelife_result_median_matrix","text":"patristic distance summary matrix datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","title":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","text":"Function compute SDM supertree (Criscuolo et al. 2006) datelifeResult object","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","text":"","code":"datelife_result_sdm_phylo(datelife_result, weighting = \"flat\", ...)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","text":"datelife_result datelifeResult object, output get_datelife_result(). weighting character vector indicating much weight give tree input SDM analysis. Choose one : weighting = \"flat\" trees equal weighting. weighting = \"taxa\" Weight proportional number taxa. weighting = \"inverse\" Weight proportional 1 / number taxa. ... Arguments passed summary_matrix_to_phylo summ_matrix summary patristic distance matrix sdm median. See details. total_distance Boolean. TRUE divide matrix half, FALSE take . use character vector indicating type age use summary. One following mean use mean node age distributions. min use minimum age node age distributions. max Choose wanna conservative; use maximum age node age distributions. target_tree phylo object. Use case want particular backbone output tree. datelife_query datelifeQuery object, output make_datelife_query().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","text":"phylo object SDM extra element: data datelifeResult object chronograms used construct SDM tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to compute the SDM supertree (Criscuolo et al. 2006) from a\ndatelifeResult object — datelife_result_sdm_phylo","text":"Criscuolo , Berry V, Douzery EJ, Gascuel O. SDM: fast distance-based approach (super) tree building phylogenomics. Syst Biol. 2006. 55(5):740. doi: 10.1080/10635150600969872.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = ","title":"Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = ","text":"Go datelifeResult object Super Distance Matrix (SDM) using weighting = \"flat\"","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = ","text":"","code":"datelife_result_sdm_matrix(datelife_result)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = ","text":"datelife_result datelifeResult object, usually output get_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = ","text":"numeric matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"Reconstruct supertree datelifeResult object using Super Distance Matrix (SDM) method.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"","code":"datelife_result_sdm_phylo(datelife_result, weighting = \"flat\", ...)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"datelife_result datelifeResult object, usually output get_datelife_result(). weighting character vector indicating much weight give tree input SDM analysis. Options : weighting = \"flat\" trees equal weighting. weighting = \"taxa\" Weight proportional number taxa. weighting = \"inverse\" Weight proportional 1 / number taxa. Defaults weighting = \"flat\". ... Arguments passed summary_matrix_to_phylo summ_matrix summary patristic distance matrix, ones obtained datelife_result_sdm_matrix() datelife_result_median_matrix(). total_distance Whether input summ_matrix stores total age distance (tip tip) distance node tip. Default TRUE, divides matrix half, FALSE take . use character vector indicating type age use summary tree. One following: \"mean\" use mean() node ages summ_matrix. \"median\" uses stats::median() age node ages summ_matrix. \"min\" use min() age node ages summ_matrix. \"max\" Choose wanna conservative; use max() age node ages summ_matrix. \"midpoint\" use mean minimum age maximum age. target_tree phylo object. Use case want specific backbone output tree. datelife_query datelifeQuery object, usually output make_datelife_query().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"supertree branch lengths proportional time, obtained summarizing individual chronograms given input datelife_result. returned object class datelifeSDM, phylo object additional $data element storing input chronograms datelifeResult object, $citation element containing citations studies input chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"Chronograms given input datelife_result summarized Super Distance Matrix (SDM) method described Criscuolo et al. (2006) doi:10.1080/10635150600969872 , implemented function ape::SDM(). resulting summary SDM clustered summary_matrix_to_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_sdm_phylo.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method. — datelife_result_sdm_phylo","text":"Criscuolo , Berry V, Douzery EJ, Gascuel O. (2006) \"SDM: fast distance-based approach (super) tree building phylogenomics\" doi:10.1080/10635150600969872 .","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_study_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Find the index of relevant studies in a cached chronogram database. — datelife_result_study_index","title":"Find the index of relevant studies in a cached chronogram database. — datelife_result_study_index","text":"datelife_result_study_index used summarize_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_study_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find the index of relevant studies in a cached chronogram database. — datelife_result_study_index","text":"","code":"datelife_result_study_index(datelife_result, cache = \"opentree_chronograms\")"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_study_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find the index of relevant studies in a cached chronogram database. — datelife_result_study_index","text":"datelife_result datelifeResult object, usually output get_datelife_result(). cache cached chronogram database.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_study_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find the index of relevant studies in a cached chronogram database. — datelife_result_study_index","text":"vector indices studies relevant information.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_variance_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute a variance matrix of a datelifeResult object. — datelife_result_variance_matrix","title":"Compute a variance matrix of a datelifeResult object. — datelife_result_variance_matrix","text":"Compute variance matrix datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_variance_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute a variance matrix of a datelifeResult object. — datelife_result_variance_matrix","text":"","code":"datelife_result_variance_matrix(datelife_result)"},{"path":"http://phylotastic.org/datelife/reference/datelife_result_variance_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute a variance matrix of a datelifeResult object. — datelife_result_variance_matrix","text":"datelife_result datelifeResult object, usually output get_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_result_variance_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute a variance matrix of a datelifeResult object. — datelife_result_variance_matrix","text":"variance matrix datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"datelife_search core DateLife function find get openly available, peer-reviewed scientific information time lineage divergence set input taxon names given character vector, newick character string, phylo multiPhylo object already processed datelifeQuery object obtained make_datelife_query().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"","code":"datelife_search( input = c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), use_tnrs = FALSE, get_spp_from_taxon = FALSE, partial = TRUE, cache = \"opentree_chronograms\", summary_format = \"phylo_all\", na_rm = FALSE, summary_print = c(\"citations\", \"taxa\"), taxon_summary = c(\"none\", \"summary\", \"matrix\"), criterion = \"taxa\" )"},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. partial Whether return exclude partially matching source chronograms, .e, match taxa given datelife_query. Options TRUE FALSE. Defaults TRUE: return matching source chronograms. cache character vector length one, name data object cache. Default \"opentree_chronograms\", data object storing Open Tree Life's database chronograms associated information. summary_format character vector length one, indicating output format results DateLife search. Available output formats : \"citations\" character vector references chronograms target taxa published (source chronograms). \"mrca\" named numeric vector recent common ancestor (mrca) ages target taxa defined input, obtained source chronograms. Names mrca vector equal citations. \"newick_all\" named character vector newick strings corresponding target chronograms derived source chronograms. Names newick_all vector equal citations. \"newick_sdm\" multiple source chronograms available. character vector single newick string corresponding target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"newick_median\" multiple source chronograms available. character vector single newick string corresponding target chronogram median source chronograms. \"phylo_sdm\" multiple source chronograms available. phylo object single target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"phylo_median\" multiple source chronograms available. phylo object single target chronogram obtained source chronograms median method. \"phylo_all\" named list phylo objects corresponding target chronogram obtained available source chronograms. Names phylo_all list correspond citations. \"phylo_biggest\" chronogram taxa. case tie, chronogram clade age closest median age equally large trees returned. \"html\" character vector html string can saved opened web browser. contains 4 column table data target taxa: mrca, number taxa, citations source chronogram newick target chronogram. \"data_frame\" 4 column data.frame data target taxa: mrca, number taxa, citations source chronograms newick string. na_rm TRUE, drops rows containing NAs datelifeResult patristic matrix; FALSE, returns NA missing entries. summary_print character vector specifying type summary information printed screen. Options : \"citations\" Prints references chronograms target taxa found. \"taxa\" Prints summary number chronograms target taxon found. \"none\" Nothing printed screen. Defaults c(\"citations\", \"taxa\"), displays . taxon_summary character vector specifying data target taxa missing source chronograms added output \"summary\" presence/absence \"matrix\". Default \"none\", information taxon_summary added output. criterion Defaults criterion = \"taxa\". Used chronogram summarizing, .e., obtaining single summary chronogram group input chronograms. summarizing approaches return single summary tree group phylogenetic trees, necessary latter form grove, roughly, sufficiently overlapping set taxa trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x . rare cases, group trees can multiple groves. argument indicates whether get grove trees (criterion = \"trees\") taxa (criterion = \"taxa\").","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"output determined argument summary_format: summary_format = \"citations\" function returns character vector references. summary_format = \"mrca\" function returns named numeric vector recent common ancestor (mrca) ages. summary_format = \"newick_[, sdm, median]\" function returns output chronograms newick strings. summary_format = \"phylo_[, sdm, median, biggest]\" function returns output chronograms phylo multiPhylo objects. summary_format = \"html\" \"data_frame\" function returns 4 column table data mrca ages, number taxa, references, output chronograms newick strings.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"one taxon name given input, get_spp_from_taxon always set TRUE.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get scientific, peer-reviewed information on time of lineage\ndivergence openly available for a given set of taxon names — datelife_search","text":"","code":"if (FALSE) { # For this example, we will set a temp working directory, but you can set # your working directory as needed: # we will use the tempdir() function to get a temporary directory: tempwd <- tempdir() # Obtain median ages from a set of source chronograms in newick format: ages <- datelife_search(c( \"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\", \"Mus musculus\" ), summary_format = \"newick_median\") # Save the tree in the temp working directory in newick format: write(ages, file = file.path(tempwd, \"some.bird.ages.txt\")) # Obtain median ages from a set of source chronograms in phylo format # Will produce same tree as above but in \"phylo\" format: ages.again <- datelife_search(c( \"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\", \"Mus musculus\" ), summary_format = \"phylo_median\") plot(ages.again) library(ape) ape::axisPhylo() mtext(\"Time (million years ago)\", side = 1, line = 2, at = (max(get(\"last_plot.phylo\", envir = .PlotPhyloEnv )$xx) * 0.5)) # Save \"phylo\" object in newick format write.tree(ages.again, file = file.path(tempwd, \"some.bird.tree.again.txt\")) # Obtain MRCA ages and target chronograms from all source chronograms # Generate an htm\"l output readable in any web browser: ages.html <- datelife_search(c( \"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\", \"Mus musculus\" ), summary_format = \"html\") write(ages.html, file = file.path(tempwd, \"some.bird.trees.html\")) system(paste(\"open\", file.path(tempwd, \"some.bird.trees.html\"))) } # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"datelife_use gets secondary calibrations available pair given taxon names, mined opentree_chronograms object, congruifies , uses date given tree topology algorithm defined dating_method. tree topology provided, attempt get one given taxon names Open Tree Life synthetic tree, using make_bold_otol_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"","code":"datelife_use(input = NULL, each = FALSE, dating_method = \"bladj\", ...)"},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames. dating_method Tree dating algorithm use. Options \"bladj\" \"pathd8\" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ). ... Arguments passed make_datelife_query use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\".","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"phylo multiPhylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"input vector taxon names, function attempt reconstruct BOLD tree make_bold_otol_tree() get tree branch lengths. fails, get Open Tree Life synthetic tree topology. function calls use_calibrations().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use.html","id":"more","dir":"Reference","previous_headings":"","what":"More","title":"Generate one or multiple chronograms for a set of given taxon names. — datelife_use","text":"output object stores used calibrations dating_method attributes(output)$datelife_calibrations attributes(output)$dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"datelife_use gets secondary calibrations available pair given taxon names, mined opentree_chronograms object, congruifies , uses date given tree topology algorithm defined dating_method. tree topology provided, attempt get one given taxon names Open Tree Life synthetic tree, using make_bold_otol_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"","code":"datelife_use_datelifequery( datelife_query = NULL, dating_method = \"bladj\", each = FALSE )"},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"datelife_query datelifeQuery object, usually output make_datelife_query(). dating_method Tree dating algorithm use. Options \"bladj\" \"pathd8\" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ). Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"phylo multiPhylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"phy branch lengths, dating_method ignores, function applies secondary calibrations date tree BLADJ algorithm. See make_bladj_tree() use_calibrations_bladj(). phy branch lengths, function can use PATHd8 algorithm. See use_calibrations_pathd8().","code":""},{"path":"http://phylotastic.org/datelife/reference/datelife_use_datelifequery.html","id":"more","dir":"Reference","previous_headings":"","what":"More","title":"Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery","text":"output object stores used calibrations dating_method attributes(output)$datelife_calibrations attributes(output)$dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/dot-get_ott_lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the lineage of a set of taxa.\n.get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE. — .get_ott_lineage","title":"Get the lineage of a set of taxa.\n.get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE. — .get_ott_lineage","text":"Get lineage set taxa. .get_ott_lineage uses rotl::taxonomy_taxon_info() include_lineage = TRUE.","code":""},{"path":"http://phylotastic.org/datelife/reference/dot-get_ott_lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the lineage of a set of taxa.\n.get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE. — .get_ott_lineage","text":"","code":".get_ott_lineage(input_ott_match)"},{"path":"http://phylotastic.org/datelife/reference/dot-get_ott_lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the lineage of a set of taxa.\n.get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE. — .get_ott_lineage","text":"input_ott_match Output check_ott_input function.","code":""},{"path":"http://phylotastic.org/datelife/reference/dot-get_ott_lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the lineage of a set of taxa.\n.get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE. — .get_ott_lineage","text":"taxonomy_taxon_info object","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_dateliferesult.html","id":null,"dir":"Reference","previous_headings":"","what":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","title":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","text":"function extracts node ages taxon pair given input$tip.labels. applies congruification method described Eastman et al. (2013) doi:10.1111/2041-210X.12051 , implemented function geiger::congruify.phylo(), create data.frame taxon pair node ages can used secondary calibrations.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_dateliferesult.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","text":"","code":"extract_calibrations_dateliferesult(input = NULL, each = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_dateliferesult.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","text":"input datelifeResult object. Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_dateliferesult.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","text":"object class calibrations, data.frame (= FALSE) list data.frames (= TRUE) node ages pair taxon names. can access input data calibrations extracted attributes(output)$chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_dateliferesult.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use congruification to extract secondary calibrations from a datelifeResult object. — extract_calibrations_dateliferesult","text":"function takes datelifeResult object calls summarize_datelife_result() summary_format = \"phylo_all\". goes datelifeResultobject aphyloormultiPhylo` object passed extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","title":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","text":"function extracts node ages taxon pair given input$tip.labels. applies congruification method described Eastman et al. (2013) doi:10.1111/2041-210X.12051 , implemented function geiger::congruify.phylo(), create data.frame taxon pair node ages can used secondary calibrations.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","text":"","code":"extract_calibrations_phylo(input = NULL, each = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","text":"input phylo multiPhylo object branch lengths proportional time. Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","text":"object class calibrations, data.frame (= FALSE) list data.frames (= TRUE) node ages pair taxon names. can access input data calibrations extracted attributes(output)$chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_calibrations_phylo.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Use congruification to extract secondary calibrations from a phylo or multiPhylo\nobject with branch lengths proportional to time. — extract_calibrations_phylo","text":"Eastman et al. (2013) \"Congruification: support time scaling large phylogenetic trees\". Methods Ecology Evolution, 4(7), 688-691, doi:10.1111/2041-210X.12051 .","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_ott_ids.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","title":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","text":"Extract numeric OTT ids character vector combines taxon names OTT ids.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_ott_ids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","text":"","code":"extract_ott_ids(x, na.rm = TRUE) # S3 method for default extract_ott_ids(x, na.rm = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/extract_ott_ids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","text":"x character vector taxon names, phylo object tree tip labels containing OTT ids. na.rm logical value indicating whether NA values stripped output.","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_ott_ids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","text":"object class numeric containing OTT ids . NULL","code":""},{"path":"http://phylotastic.org/datelife/reference/extract_ott_ids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. — extract_ott_ids","text":"","code":"if (FALSE) # This is a flag for package development. You are welcome to run the example. canis <- rotl::tnrs_match_names(\"canis\") canis_taxonomy <- rotl::taxonomy_subtree(canis$ott_id) #> Error in check_ott_ids(ott_id): object 'canis' not found my_ott_ids <- extract_ott_ids(x = canis_taxonomy$tip_label) #> Error in extract_ott_ids(x = canis_taxonomy$tip_label): object 'canis_taxonomy' not found # Get the problematic elements from input canis_taxonomy$tip_label[attr(my_ott_ids, \"na.action\")] #> Error in eval(expr, envir, enclos): object 'canis_taxonomy' not found # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/felid_gdr_phylo_all.html","id":null,"dir":"Reference","previous_headings":"","what":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","title":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","text":"datelifeSummary datelifeResult object Felidae species.","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_gdr_phylo_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","text":"","code":"felid_gdr_phylo_all"},{"path":"http://phylotastic.org/datelife/reference/felid_gdr_phylo_all.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","text":"list three elements, containing summary datelifeResult object phylo_all List subset chronograms phylo format taxon_distribution data frame taxon presence across subset chronograms absent_taxa dataframe names taxon found chronogram","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_gdr_phylo_all.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_gdr_phylo_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"datelifeSummary of a datelifeResult object of all Felidae species. — felid_gdr_phylo_all","text":"Generated : felid_spp <- make_datelife_query(input = \"felidae\", get_spp_from_taxon = TRUE) felid_gdr <- get_datelife_result(input = felid_spp, get_spp_from_taxon = TRUE) felid_gdr_phylo_all <- summarize_datelife_result(datelife_result = felid_gdr, taxon_summary = \"summary\", summary_format = \"phylo_all\", datelife_query = felid_spp) usethis::use_data(felid_gdr_phylo_all)","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_sdm.html","id":null,"dir":"Reference","previous_headings":"","what":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","title":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","text":"SDM tree datelifeResult object Felidae species.","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_sdm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","text":"","code":"felid_sdm"},{"path":"http://phylotastic.org/datelife/reference/felid_sdm.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","text":"list two elements, containing summary datelifeResult object phy ultrametric phylo object SDM tree. data datelifeResult object data used construct phy","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_sdm.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/felid_sdm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"SDM tree of a datelifeResult object of all Felidae species. — felid_sdm","text":"Generated : felid_spp <- make_datelife_query(input = \"felidae\", get_spp_from_taxon = TRUE) felid_gdr <- get_datelife_result(input = felid_spp, get_spp_from_taxon = TRUE) felid_sdm <- datelife_result_sdm_phylo(felid_gdr) usethis::use_data(felid_sdm)","code":""},{"path":"http://phylotastic.org/datelife/reference/filter_for_grove.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter a datelifeResult object to find the largest grove. — filter_for_grove","title":"Filter a datelifeResult object to find the largest grove. — filter_for_grove","text":"Filter datelifeResult object find largest grove.","code":""},{"path":"http://phylotastic.org/datelife/reference/filter_for_grove.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter a datelifeResult object to find the largest grove. — filter_for_grove","text":"","code":"filter_for_grove(datelife_result, criterion = \"taxa\", n = 2)"},{"path":"http://phylotastic.org/datelife/reference/filter_for_grove.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter a datelifeResult object to find the largest grove. — filter_for_grove","text":"datelife_result datelifeResult object. needed criterion = \"taxa\". criterion Defaults criterion = \"taxa\". Used chronogram summarizing, .e., obtaining single summary chronogram group input chronograms. summarizing approaches return single summary tree group phylogenetic trees, necessary latter form grove, roughly, sufficiently overlapping set taxa trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x . rare cases, group trees can multiple groves. argument indicates whether get grove trees (criterion = \"trees\") taxa (criterion = \"taxa\"). n degree taxon name overlap among input chronograms. Defaults n = 2, .e., least two overlapping taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/filter_for_grove.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter a datelifeResult object to find the largest grove. — filter_for_grove","text":"datelifeResult object filtered include one grove trees.","code":""},{"path":"http://phylotastic.org/datelife/reference/force_ultrametric.html","id":null,"dir":"Reference","previous_headings":"","what":"Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric(). — force_ultrametric","title":"Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric(). — force_ultrametric","text":"Force non-ultrametric phylo object ultrametric phytools::force.ultrametric().","code":""},{"path":"http://phylotastic.org/datelife/reference/force_ultrametric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric(). — force_ultrametric","text":"","code":"force_ultrametric(phy)"},{"path":"http://phylotastic.org/datelife/reference/force_ultrametric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric(). — force_ultrametric","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/force_ultrametric.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric(). — force_ultrametric","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get secondary calibrations from a chronogram database for a set of given taxon names — get_all_calibrations","title":"Get secondary calibrations from a chronogram database for a set of given taxon names — get_all_calibrations","text":"get_all_calibrations performs datelife_search() gets divergence times (.e., secondary calibrations) chronogram database taxon name pair given input. get_all_calibrations performs datelife_search() gets divergence times (.e., secondary calibrations) chronogram database taxon name pair given input.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get secondary calibrations from a chronogram database for a set of given taxon names — get_all_calibrations","text":"","code":"get_all_calibrations(input = NULL, each = FALSE) get_all_calibrations(input = NULL, each = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/get_all_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get secondary calibrations from a chronogram database for a set of given taxon names — get_all_calibrations","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get secondary calibrations from a chronogram database for a set of given taxon names — get_all_calibrations","text":"object class calibrations, data.frame (= FALSE) list data.frames (= TRUE) node ages pair taxon names. can access input data calibrations extracted attributes(output)$chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_descendant_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_all_descendant_species","title":"Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_all_descendant_species","text":"less thorough get_open_tree_species(), much faster. uses fact something just two names (genus species) assume something single species; two names, assumed subspecies goes one level hierarchy. return subspecies species.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_descendant_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_all_descendant_species","text":"","code":"get_all_descendant_species(taxon_name, ott_id)"},{"path":"http://phylotastic.org/datelife/reference/get_all_descendant_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_all_descendant_species","text":"taxon_name character vector providing inclusive taxonomic name. ott_id numeric vector providig Open Tree Taxonomic id number taxonomic name. provided, taxon_name ignored. Used context OTT detect invalid taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_all_descendant_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_all_descendant_species","text":"list unique OTT names OTT ids species within provided taxon.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_best_grove.html","id":null,"dir":"Reference","previous_headings":"","what":"Get grove from a datelifeResult object that can be converted to phylo\nfrom a median summary matrix — get_best_grove","title":"Get grove from a datelifeResult object that can be converted to phylo\nfrom a median summary matrix — get_best_grove","text":"Get grove datelifeResult object can converted phylo median summary matrix","code":""},{"path":"http://phylotastic.org/datelife/reference/get_best_grove.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get grove from a datelifeResult object that can be converted to phylo\nfrom a median summary matrix — get_best_grove","text":"","code":"get_best_grove(datelife_result, criterion = \"taxa\", n = 2)"},{"path":"http://phylotastic.org/datelife/reference/get_best_grove.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get grove from a datelifeResult object that can be converted to phylo\nfrom a median summary matrix — get_best_grove","text":"datelife_result datelifeResult object. needed criterion = \"taxa\". criterion Defaults criterion = \"taxa\". Used chronogram summarizing, .e., obtaining single summary chronogram group input chronograms. summarizing approaches return single summary tree group phylogenetic trees, necessary latter form grove, roughly, sufficiently overlapping set taxa trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x . rare cases, group trees can multiple groves. argument indicates whether get grove trees (criterion = \"trees\") taxa (criterion = \"taxa\"). n degree taxon name overlap among input chronograms. Defaults n = 2, .e., least two overlapping taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_best_grove.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get grove from a datelifeResult object that can be converted to phylo\nfrom a median summary matrix — get_best_grove","text":"list two elements: best_grove datelifeResult object filtered include one grove trees can summarized median sdm. overlap degree taxon names overlap among trees best grove.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_multiphylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the tree with the most tips from a multiPhylo object: the biggest tree. — get_biggest_multiphylo","title":"Get the tree with the most tips from a multiPhylo object: the biggest tree. — get_biggest_multiphylo","text":"Get tree tips multiPhylo object: biggest tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_multiphylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the tree with the most tips from a multiPhylo object: the biggest tree. — get_biggest_multiphylo","text":"","code":"get_biggest_multiphylo(trees)"},{"path":"http://phylotastic.org/datelife/reference/get_biggest_multiphylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the tree with the most tips from a multiPhylo object: the biggest tree. — get_biggest_multiphylo","text":"trees list trees multiPhylo generic list object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_multiphylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the tree with the most tips from a multiPhylo object: the biggest tree. — get_biggest_multiphylo","text":"largest tree given trees, phylo object additional $citation element containing reference original publication.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the tree with the most tips: the biggest tree. — get_biggest_multiphylo","title":"Get the tree with the most tips: the biggest tree. — get_biggest_multiphylo","text":"Get tree tips: biggest tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the tree with the most tips: the biggest tree. — get_biggest_multiphylo","text":"","code":"get_biggest_multiphylo(trees)"},{"path":"http://phylotastic.org/datelife/reference/get_biggest_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the tree with the most tips: the biggest tree. — get_biggest_multiphylo","text":"trees list trees multiPhylo plain list object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_biggest_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the tree with the most tips: the biggest tree. — get_biggest_multiphylo","text":"phylo object citation slot citation biggest tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_bold_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","title":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","text":"get_bold_data uses taxon names tree topology, character vector names datelifeQuery object, search genetic markers Barcode Life Database (BOLD).","code":""},{"path":"http://phylotastic.org/datelife/reference/get_bold_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","text":"","code":"get_bold_data( input = c(\"Rhea americana\", \"Struthio camelus\", \"Gallus gallus\"), marker = \"COI\", ... )"},{"path":"http://phylotastic.org/datelife/reference/get_bold_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). marker character vector indicating gene BOLD system used branch length estimation. searches \"COI\" marker default. ... Arguments passed get_otol_synthetic_tree otol_version Version Open Tree Life use resolve Defaults TRUE. Whether resolve tree random . ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_bold_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","text":"phylo object. enough BOLD sequences available input taxon names, function returns tree branch lengths proportional relative substitution rate. enough BOLD sequences available input taxon names, function returns topology given input, synthetic Open Tree Life taxon names given input, obtained get_otol_synthetic_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_bold_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. — get_bold_data","text":"input phylo object newick string, used backbone topology. input character vector taxon names, induced synthetic OpenTree subtree used backbone.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_datelifequery.html","id":null,"dir":"Reference","previous_headings":"","what":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","title":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","text":"function searches DateLife's local database phylogenetic trees branch lengths proportional time (chronograms) datelife_search(), extracts available node ages pair given taxon names extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_datelifequery.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","text":"","code":"get_calibrations_datelifequery(datelife_query = NULL, each = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_datelifequery.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","text":"datelife_query datelifeQuery object. Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_datelifequery.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","text":"object class calibrations, data.frame (= FALSE) list data.frames (= TRUE) node ages pair taxon names. can access input data calibrations extracted attributes(output)$chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_datelifequery.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search and extract available secondary calibrations for taxon names in a given\ndatelifeQuery object — get_calibrations_datelifequery","text":"function calls datelife_search() summary_format = \"phylo_all\" get chronograms database containing least two taxa input, generates phylo multiPhylo object object passed extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_vector.html","id":null,"dir":"Reference","previous_headings":"","what":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","title":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","text":"function searches DateLife's local database phylogenetic trees branch lengths proportional time (chronograms) datelife_search(), extracts available node ages pair given taxon names extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_vector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","text":"","code":"get_calibrations_vector(input = NULL, each = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_vector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","text":"input character vector taxon names. Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_vector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","text":"object class calibrations, data.frame (= FALSE) list data.frames (= TRUE) node ages pair taxon names. can access input data calibrations extracted attributes(output)$chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_calibrations_vector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search and extract secondary calibrations for a given character\nvector of taxon names — get_calibrations_vector","text":"function calls datelife_search() summary_format = \"phylo_all\" get chronograms database containing least two taxa input, generates phylo multiPhylo object object passed extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_dated_otol_induced_subtree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","title":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","text":"Get dated OpenTree induced synthetic subtree set given taxon names, blackrim's FePhyFoFum service.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_dated_otol_induced_subtree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","text":"","code":"get_dated_otol_induced_subtree(input = NULL, ott_ids = NULL, ...)"},{"path":"http://phylotastic.org/datelife/reference/get_dated_otol_induced_subtree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). ... Arguments passed check_ott_input","code":""},{"path":"http://phylotastic.org/datelife/reference/get_dated_otol_induced_subtree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","text":"phylo object edge length proportional time Myrs. return NA ott_id invalid.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_dated_otol_induced_subtree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. — get_dated_otol_induced_subtree","text":"OpenTree dated tree Stephen Smith's OpenTree scaling service https://github.com/FePhyFoFum/gophy want make LTT plot dated OpenTree tree need get rid singleton nodes ape::collapse.singles() also probably phytools::force.ultrametric().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a patristic matrix of time of lineage divergence data for a given set of taxon names — get_datelife_result","title":"Get a patristic matrix of time of lineage divergence data for a given set of taxon names — get_datelife_result","text":"get_datelife_result takes input vector taxon names, newick string, phylo object, adatelifeQuery object. searches chronogram database specified cache chronograms matching two given taxon names. matching chronogram, extracts time lineage divergence data stores patristic matrix. lists resulting patristic matrices. list element named study citation source chronogram.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a patristic matrix of time of lineage divergence data for a given set of taxon names — get_datelife_result","text":"","code":"get_datelife_result( input = NULL, partial = TRUE, cache = \"opentree_chronograms\", update_opentree_chronograms = FALSE, ... )"},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a patristic matrix of time of lineage divergence data for a given set of taxon names — get_datelife_result","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). partial Whether return exclude partially matching source chronograms, .e, match taxa given datelife_query. Options TRUE FALSE. Defaults TRUE: return matching source chronograms. cache character vector length one, name data object cache. Default \"opentree_chronograms\", data object storing Open Tree Life's database chronograms associated information. update_opentree_chronograms Whether update chronogram database . Defaults FALSE. ... Arguments passed make_datelife_query use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\".","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a patristic matrix of time of lineage divergence data for a given set of taxon names — get_datelife_result","text":"datelifeResult object -- named list patristic matrices.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result_datelifequery.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","title":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","text":"Get list patristic matrices given datelifeQuery object","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result_datelifequery.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","text":"","code":"get_datelife_result_datelifequery( datelife_query = NULL, partial = TRUE, cache = \"opentree_chronograms\", update_opentree_chronograms = FALSE, ... )"},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result_datelifequery.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","text":"datelife_query datelifeQuery object, usually output make_datelife_query(). partial Whether return exclude partially matching source chronograms, .e, match taxa given datelife_query. Options TRUE FALSE. Defaults TRUE: return matching source chronograms. cache character vector length one, name data object cache. Default \"opentree_chronograms\", data object storing Open Tree Life's database chronograms associated information. update_opentree_chronograms Whether update chronogram database . Defaults FALSE. ... Arguments passed make_datelife_query input Taxon names one following: character vector taxon names taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\".","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result_datelifequery.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","text":"datelifeResult object -- named list patristic matrices.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_datelife_result_datelifequery.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get a list of patristic matrices from a given datelifeQuery object — get_datelife_result_datelifequery","text":"just one taxon name input$cleaned_names, function run make_datelife_query() setting get_spp_from_taxon = TRUE. datelifeQuery used input can accessed attributes(datelifeResult)$query.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_fossil_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the ages for a taxon from PBDB — get_fossil_range","title":"Get the ages for a taxon from PBDB — get_fossil_range","text":"uses Paleobiology Database's API gather information ages specimens taxon. also look descendants taxon. fixes name misspellings possible.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_fossil_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the ages for a taxon from PBDB — get_fossil_range","text":"","code":"get_fossil_range(taxon, recent = FALSE, assume_recent_if_missing = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/get_fossil_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the ages for a taxon from PBDB — get_fossil_range","text":"taxon scientific name taxon want range occurrences recent TRUE, forces minimum age zero assume_recent_if_missing TRUE, taxon missing pbdb assumed recent","code":""},{"path":"http://phylotastic.org/datelife/reference/get_fossil_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the ages for a taxon from PBDB — get_fossil_range","text":"data.frame max_ma min_ma specimens","code":""},{"path":"http://phylotastic.org/datelife/reference/get_goodmatrices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm(). — get_goodmatrices","title":"Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm(). — get_goodmatrices","text":"Get indices good matrices apply Super Distance Matrix (SDM) method make_sdm().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_goodmatrices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm(). — get_goodmatrices","text":"","code":"get_goodmatrices(unpadded.matrices)"},{"path":"http://phylotastic.org/datelife/reference/get_goodmatrices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm(). — get_goodmatrices","text":"unpadded.matrices list patristic matrices, datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_goodmatrices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm(). — get_goodmatrices","text":"numeric vector good matrix indices unpadded.matrices.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_mrbayes_node_constraints.html","id":null,"dir":"Reference","previous_headings":"","what":"Makes a block of node constraints and node calibrations for a MrBayes run file\nfrom a list of taxa and ages, or from a dated tree — get_mrbayes_node_constraints","title":"Makes a block of node constraints and node calibrations for a MrBayes run file\nfrom a list of taxa and ages, or from a dated tree — get_mrbayes_node_constraints","text":"Makes block node constraints node calibrations MrBayes run file list taxa ages, dated tree","code":""},{"path":"http://phylotastic.org/datelife/reference/get_mrbayes_node_constraints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Makes a block of node constraints and node calibrations for a MrBayes run file\nfrom a list of taxa and ages, or from a dated tree — get_mrbayes_node_constraints","text":"","code":"get_mrbayes_node_constraints( constraint = NULL, taxa = NULL, missing_taxa = NULL, ncalibration = NULL, age_distribution = \"fixed\", root_calibration = FALSE, mrbayes_constraints_file = NULL, clockratepr = \"prset clockratepr = fixed(1);\" )"},{"path":"http://phylotastic.org/datelife/reference/get_mrbayes_node_constraints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Makes a block of node constraints and node calibrations for a MrBayes run file\nfrom a list of taxa and ages, or from a dated tree — get_mrbayes_node_constraints","text":"constraint constraint tree: phylo object newick character string, without branch lengths. taxa character vector taxon names maintained tree missing_taxa tree, data frame vector enlisting missing taxa want include. tree Either phylo object newick character string. contains taxa want end, missing non missing. tree used hard constraint. data.frame contains two columns named \"taxon\" \"clade\". first one contains character vector missing taxon names. second one contains character numeric vector nodes constraint tree taxon assigned. character vector contains names missing taxa. added random constraint tree. ncalibration node calibrations: phylo object branch lengths proportional time; case nodes ncalibration used calibration points. Alternatively, list two elements: first character vector node names phy calibrate; second numeric vector corresponding ages use calibrations. age_distribution character string specifying type calibration. \"fixed\" \"uniform\" implemented now. fixed age given ncalibration used fixed age. lognormal age given ncalibration used mean age. standard deviation can provided. # still need add option. default, 95 CI sd used. uniform age given ncalibration used mean age. min_age = 0.9 * mean age, max_age = 1.1 * mean age. root_calibration Used set calibration root . Default FALSE. relevant ncalibration specified. mrbayes_constraints_file NULL character vector indicating name mrbayes constraint /calibration block file. clockratepr character vector indicating clockrateprior used.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_mrbayes_node_constraints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Makes a block of node constraints and node calibrations for a MrBayes run file\nfrom a list of taxa and ages, or from a dated tree — get_mrbayes_node_constraints","text":"set MrBayes constraints /calibration commands printed console character strings text file specified mrbayes_constraints_file.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all chronograms from Open Tree of Life database using direct call from Open Tree API — get_opentree_chronograms","title":"Get all chronograms from Open Tree of Life database using direct call from Open Tree API — get_opentree_chronograms","text":"Get chronograms Open Tree Life database using direct call Open Tree API","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all chronograms from Open Tree of Life database using direct call from Open Tree API — get_opentree_chronograms","text":"","code":"get_opentree_chronograms(max_tree_count = \"all\") get_otol_chronograms(max_tree_count = \"all\")"},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all chronograms from Open Tree of Life database using direct call from Open Tree API — get_opentree_chronograms","text":"max_tree_count Default \"\", gets available chronograms. testing purposes, numeric value indicating max number trees cached.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all chronograms from Open Tree of Life database using direct call from Open Tree API — get_opentree_chronograms","text":"list 4 elements: authors list lists author names original studies published chronograms currently stored Open Tree Life database. curators list lists curator names uploaded chronograms Open Tree Life database. studies list study identifiers original studies published chronograms currently stored Open Tree Life database. trees multiPhylo object storing chronograms Open Tree Life database. update character vector indicating time database object last updated. version character vector indicating datelife package version object last updated.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms_slow.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms_slow","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms_slow","text":"Get chronograms Open Tree Life database","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms_slow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms_slow","text":"","code":"get_opentree_chronograms_slow(max_tree_count = \"all\")"},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms_slow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms_slow","text":"max_tree_count Default \"\", gets available chronograms. testing purposes, numeric value indicating max number trees cached.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_chronograms_slow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms_slow","text":"list 4 elements: authors list lists author names original studies published chronograms currently stored Open Tree Life database. curators list lists curator names uploaded chronograms Open Tree Life database. studies list study identifiers original studies published chronograms currently stored Open Tree Life database. trees multiPhylo object storing chronograms Open Tree Life database. update character vector indicating time database object last updated. version character vector indicating datelife package version object last updated.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_opentree_species","title":"Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_opentree_species","text":"Get species belonging taxon Open Tree Life Taxonomy (OTT)","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_opentree_species","text":"","code":"get_opentree_species(taxon_name, ott_id, synth_tree_only = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/get_opentree_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_opentree_species","text":"taxon_name character vector providing inclusive taxonomic name. ott_id numeric vector providig Open Tree Taxonomic id number taxonomic name. provided, taxon_name ignored. Used context OTT detect invalid taxon names. synth_tree_only Whether include species synthetic Open Tree Life . Default TRUE.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_opentree_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) — get_opentree_species","text":"list unique OTT names OTT ids species within provided taxon.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_chronograms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms","text":"Get chronograms Open Tree Life database","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_chronograms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms","text":"","code":"get_opentree_chronograms(max_tree_count = \"all\")"},{"path":"http://phylotastic.org/datelife/reference/get_otol_chronograms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms","text":"max_tree_count Default \"\", gets available chronograms. testing purposes, numeric value indicating max number trees cached.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_chronograms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all chronograms from Open Tree of Life database — get_opentree_chronograms","text":"list 4 elements: authors list lists author names original studies published chronograms currently stored Open Tree Life database. curators list lists curator names uploaded chronograms Open Tree Life database. studies list study identifiers original studies published chronograms currently stored Open Tree Life database. trees multiPhylo object storing chronograms Open Tree Life database.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_synthetic_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get an Open Tree of Life synthetic subtree of a set of given taxon names. — get_otol_synthetic_tree","title":"Get an Open Tree of Life synthetic subtree of a set of given taxon names. — get_otol_synthetic_tree","text":"Get Open Tree Life synthetic subtree set given taxon names.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_synthetic_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get an Open Tree of Life synthetic subtree of a set of given taxon names. — get_otol_synthetic_tree","text":"","code":"get_otol_synthetic_tree( input = NULL, ott_ids = NULL, otol_version = \"v3\", resolve = FALSE, ... )"},{"path":"http://phylotastic.org/datelife/reference/get_otol_synthetic_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get an Open Tree of Life synthetic subtree of a set of given taxon names. — get_otol_synthetic_tree","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). otol_version Version Open Tree Life use resolve Defaults TRUE. Whether resolve tree random . ... Arguments passed check_ott_input","code":""},{"path":"http://phylotastic.org/datelife/reference/get_otol_synthetic_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get an Open Tree of Life synthetic subtree of a set of given taxon names. — get_otol_synthetic_tree","text":"phylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","title":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","text":"Use instead rotl::tol_subtree() taxa synthesis tree still need get species induced OpenTree subtree","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","text":"","code":"get_ott_children(input = NULL, ott_ids = NULL, ott_rank = \"species\", ...)"},{"path":"http://phylotastic.org/datelife/reference/get_ott_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). ott_rank character vector ranks wanna get lineage children . ... arguments pass get_valid_children().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","text":"data.frame object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_children.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and\nyou still need to get all species or an induced OpenTree subtree — get_ott_children","text":"","code":"# An example with the dog genus: # It is currently not possible to get an OpenTree subtree of a taxon that is # missing from the OpenTree synthetic tree. # The dog genus is not monophyletic in the OpenTree synthetic tree, so in # practice, it has no node to extract a subtree from. tnrs <- tnrs_match(\"Canis\") #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% if (FALSE) # This is a flag for package development. You are welcome to run the example. rotl::tol_subtree(tnrs$ott_id[1]) #> Error: HTTP failure: 400 #> [/v3/tree_of_life/subtree] Error: node_id was not found (broken taxon). # end dontrun ids <- tnrs$ott_id[1] names(ids) <- tnrs$unique_name children <- get_ott_children(ott_ids = ids) # or #> | | | 0% | |======================================================================| 100% children <- get_ott_children(input = \"Canis\") #> 'input' is not a 'datelifeQuery' object. #> ---> Phylo-processing 'input'. #> * 'input' is not a phylogeny. #> ---> Making a DateLife query. #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> ---> Working with the following taxon: Canis. #> DateLife query made! #> | | | 0% | |======================================================================| 100% if (!is.na(children)) { str(children) ids <- children$Canis$ott_id names(ids) <- rownames(children$Canis) tree_children <- datelife::get_otol_synthetic_tree(ott_ids = ids) plot(tree_children, cex = 0.3) } #> List of 1 #> $ Canis:'data.frame':\t11 obs. of 2 variables: #> ..$ ott_id: int [1:11] 3612500 5835572 113383 752755 621168 666235 621176 247331 247341 346723 ... #> ..$ rank : chr [1:11] \"species\" \"species\" \"species\" \"species\" ... #> ... Getting an OpenTree induced synthetic subtree. #> OpenTree synthetic tree of 'input' taxa is not fully resolved (5 nodes/11 tips). #> Success! # An example with flowering plants: if (FALSE) # This is a flag for package development. You are welcome to run the example. oo <- get_ott_children(input = \"magnoliophyta\", ott_rank = \"order\") # Get the number of orders of flowering plants that we have sum(oo$Magnoliophyta$rank == \"order\") #> Error in eval(expr, envir, enclos): object 'oo' not found # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/get_ott_clade.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or\nseveral given taxonomic ranks from one or more input taxa. — get_ott_clade","title":"Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or\nseveral given taxonomic ranks from one or more input taxa. — get_ott_clade","text":"Get Open Tree Life Taxonomic identifiers (OTT ids) name one several given taxonomic ranks one input taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_clade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or\nseveral given taxonomic ranks from one or more input taxa. — get_ott_clade","text":"","code":"get_ott_clade(input = NULL, ott_ids = NULL, ott_rank = \"family\")"},{"path":"http://phylotastic.org/datelife/reference/get_ott_clade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or\nseveral given taxonomic ranks from one or more input taxa. — get_ott_clade","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). ott_rank character vector ranks wanna get lineage children .","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_clade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or\nseveral given taxonomic ranks from one or more input taxa. — get_ott_clade","text":"list named numeric vectors OTT ids input requested ranks.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","title":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","text":"Get Open Tree Life Taxonomic identifier (OTT id) name lineages one input taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","text":"","code":"get_ott_lineage(input = NULL, ott_ids = NULL)"},{"path":"http://phylotastic.org/datelife/reference/get_ott_lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","text":"list named numeric vectors ott ids input clades belongs .","code":""},{"path":"http://phylotastic.org/datelife/reference/get_ott_lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages\nfrom one or more input taxa. — get_ott_lineage","text":"","code":"if (FALSE) # This is a flag for package development. You are welcome to run the example. taxa <- c(\"Homo\", \"Bacillus anthracis\", \"Apis\", \"Salvia\") lin <- get_ott_lineage(taxa) #> Error in check_ott_input(input, ott_ids): object 'taxa' not found lin #> Error in eval(expr, envir, enclos): object 'lin' not found # Look up an unknown OTT id: get_ott_lineage(ott_id = 454749) #> | | | 0% | |======================================================================| 100% #> $`Discelium nudum` #> ott_ids ott_ranks #> Discelium \"508293\" \"genus\" #> Disceliaceae \"538343\" \"family\" #> Funariales \"821347\" \"order\" #> Funariidae \"620630\" \"subclass\" #> Bryopsida \"821346\" \"class\" #> Bryophytina \"471195\" \"no rank\" #> Bryophyta \"246594\" \"phylum\" #> Embryophyta \"56610\" \"no rank\" #> Streptophyta \"916750\" \"phylum\" #> Chloroplastida \"361838\" \"kingdom\" #> Archaeplastida \"5268475\" \"kingdom\" #> Eukaryota \"304358\" \"domain\" #> cellular organisms \"93302\" \"no rank\" #> life \"805080\" \"no rank\" #> # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/get_sdm.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","title":"Get a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"Get Super Distance Matrix (SDM) list good matrices obtained get_goodmatrices()","code":""},{"path":"http://phylotastic.org/datelife/reference/get_sdm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"","code":"make_sdm(unpadded.matrices, weighting = \"flat\")"},{"path":"http://phylotastic.org/datelife/reference/get_sdm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"unpadded.matrices list patristic matrices, datelifeResult object. weighting character vector indicating much weight give tree input SDM analysis. Options : weighting = \"flat\" trees equal weighting. weighting = \"taxa\" Weight proportional number taxa. weighting = \"inverse\" Weight proportional 1 / number taxa. Defaults weighting = \"flat\".","code":""},{"path":"http://phylotastic.org/datelife/reference/get_sdm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_sdm_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Get good matrices for SDM — get_sdm_matrix","title":"Get good matrices for SDM — get_sdm_matrix","text":"Get good matrices SDM","code":""},{"path":"http://phylotastic.org/datelife/reference/get_sdm_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get good matrices for SDM — get_sdm_matrix","text":"","code":"get_sdm_matrix(datelife_result)"},{"path":"http://phylotastic.org/datelife/reference/get_sdm_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get good matrices for SDM — get_sdm_matrix","text":"datelife_result datelifeResult object, output get_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_sdm_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get good matrices for SDM — get_sdm_matrix","text":"numeric matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_subset_array_dispatch.html","id":null,"dir":"Reference","previous_headings":"","what":"Figure out which subset function to use. — get_subset_array_dispatch","title":"Figure out which subset function to use. — get_subset_array_dispatch","text":"get_subset_array_dispatch used inside get_datelife_result()","code":""},{"path":"http://phylotastic.org/datelife/reference/get_subset_array_dispatch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Figure out which subset function to use. — get_subset_array_dispatch","text":"","code":"get_subset_array_dispatch( study_element, taxa, phy = NULL, phy4 = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/get_subset_array_dispatch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Figure out which subset function to use. — get_subset_array_dispatch","text":"study_element thing passed : array phylo object serve reference congruification. taxa Vector taxon names get subset . phy user tree congruify phylo object (ape). phy4 user tree congruify phylo4 format (phylobase). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_subset_array_dispatch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Figure out which subset function to use. — get_subset_array_dispatch","text":"patristic matrix ages target taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_taxon_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a taxon summary of a datelifeResult object. — get_taxon_summary","title":"Get a taxon summary of a datelifeResult object. — get_taxon_summary","text":"Get taxon summary datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_taxon_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a taxon summary of a datelifeResult object. — get_taxon_summary","text":"","code":"get_taxon_summary(datelife_result = NULL, datelife_query = NULL)"},{"path":"http://phylotastic.org/datelife/reference/get_taxon_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a taxon summary of a datelifeResult object. — get_taxon_summary","text":"datelife_result datelifeResult object, usually output get_datelife_result(). datelife_query datelifeQuery object, usually output make_datelife_query().","code":""},{"path":"http://phylotastic.org/datelife/reference/get_taxon_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a taxon summary of a datelifeResult object. — get_taxon_summary","text":"datelifeTaxonSummary object, list 4 elements: $matrix Data presence/absence matrix taxon names across chronograms. $summary data.frame taxon names row.names() two columns, one number chronograms contain taxon name one total number chronograms least 2 taxon names. $summary2 data.frame chronogram citations row.names() two columns, one number taxon names found chronogram one total number taxon names. $absent_taxa character vector taxon names found chronogram database.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_tnrs_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Process a character vector of taxon names with TNRS — get_tnrs_names","title":"Process a character vector of taxon names with TNRS — get_tnrs_names","text":"make_datelife_query2 always uses TNRS (Taxonomic Name Resolution Service process input taxon names, correct misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names()).","code":""},{"path":"http://phylotastic.org/datelife/reference/get_tnrs_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process a character vector of taxon names with TNRS — get_tnrs_names","text":"","code":"get_tnrs_names( input = c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), reference_taxonomy = \"ott\", ... )"},{"path":"http://phylotastic.org/datelife/reference/get_tnrs_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process a character vector of taxon names with TNRS — get_tnrs_names","text":"input Taxon names character vector taxon names. Two names can provided single comma separated string concatenated c(). reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\". ... Arguments passed rotl::tnrs_match_names context_name name taxonomic context searched (length-one character vector NULL). Must match (case sensitive) one values returned tnrs_contexts. Default \"life\". do_approximate_matching logical indicating whether perform approximate string (.k.. “fuzzy”) matching. Using FALSE greatly improve speed. Default, however, TRUE. ids vector ids use identifying names. assigned name names array. ids provided, ids names must identical length. include_suppressed Ordinarily, quasi-taxa, incertae sedis buckets non-OTUs, suppressed TNRS results. parameter true, quasi-taxa allowed possible TNRS results.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_tnrs_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process a character vector of taxon names with TNRS — get_tnrs_names","text":"datelifeTNRS object, list three elements: $cleaned_names character vector names provided input. $tnrs_names character vector taxon names processed TNRS. $ott_ids numeric vector Open Tree Life Taxonomy (OTT) ids.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"Extract valid children given taxonomic name(s) Open Tree Life Taxonomic identifiers (OTT ids) taxonomic source.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"","code":"get_valid_children(input = NULL, ott_ids = NULL, reference_taxonomy = \"ncbi\")"},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match(). reference_taxonomy character vector desired taxonomic sources. Options \"ncbi\", \"gbif\" \"irmng\". value retrieve data taxonomic sources. function defaults \"ncbi\".","code":""},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"named list containing valid taxonomic children given taxonomic name(s).","code":""},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"GBIF taxonomies contain deprecated taxa marked Open Tree Life Taxonomy. relying mainly NCBI taxonomy now.","code":""},{"path":"http://phylotastic.org/datelife/reference/get_valid_children.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract valid children from given taxonomic name(s) or Open Tree of Life\nTaxonomic identifiers (OTT ids) from a taxonomic source. — get_valid_children","text":"","code":"# genus Dictyophyllidites with ott id = 6003921 has only extinct children # in cases like this the same name will be returned tti <- rotl::taxonomy_taxon_info(6003921, include_children = TRUE) gvc <- get_valid_children(ott_ids = 6003921) #> | | | 0% | |======================================================================| 100% # More examples: get_valid_children(ott_ids = 769681) # Psilotopsida #> | | | 0% | |======================================================================| 100% #> $Tracheophyta #> $Tracheophyta$children #> ott_id rank #> Euphyllophyta 1007992 no rank #> Lycopodiopsida 144795 class #> #> $Tracheophyta$is_monotypic #> [1] FALSE #> #> get_valid_children(ott_ids = 56601) # Marchantiophyta #> | | | 0% | |======================================================================| 100% #> $Marchantiophyta #> $Marchantiophyta$children #> ott_id rank #> Jungermanniopsida 991930 class #> Marchantiopsida 991932 class #> Haplomitriopsida 339229 class #> #> $Marchantiophyta$is_monotypic #> [1] FALSE #> #>"},{"path":"http://phylotastic.org/datelife/reference/input_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process a phylo object or a character string to determine if it's correct newick — input_process","title":"Process a phylo object or a character string to determine if it's correct newick — input_process","text":"Process phylo object character string determine correct newick","code":""},{"path":"http://phylotastic.org/datelife/reference/input_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process a phylo object or a character string to determine if it's correct newick — input_process","text":"","code":"input_process(input)"},{"path":"http://phylotastic.org/datelife/reference/input_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process a phylo object or a character string to determine if it's correct newick — input_process","text":"input Taxon names one following: character vector taxon names taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string.","code":""},{"path":"http://phylotastic.org/datelife/reference/input_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process a phylo object or a character string to determine if it's correct newick — input_process","text":"phylo object NA input tree .","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if input is a datelifeQuery object — is_datelife_query","title":"Check if input is a datelifeQuery object — is_datelife_query","text":"is_datelife_query checks two things TRUE FALSE. First, input class datelifeQuery. Second, input list contains least two elements datelifeQuery object: cleaned_names character vector taxon names. phy Either NA phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if input is a datelifeQuery object — is_datelife_query","text":"","code":"is_datelife_query(input)"},{"path":"http://phylotastic.org/datelife/reference/is_datelife_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if input is a datelifeQuery object — is_datelife_query","text":"input object checked object essential properties 'datelifeQuery' object.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if input is a datelifeQuery object — is_datelife_query","text":"determined second condition.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_query.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check if input is a datelifeQuery object — is_datelife_query","text":"object correct format class different datelifeQuery, class modified.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_result_empty.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if we obtained an empty search with the given taxon name(s). — is_datelife_result_empty","title":"Check if we obtained an empty search with the given taxon name(s). — is_datelife_result_empty","text":"Check obtained empty search given taxon name(s).","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_result_empty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if we obtained an empty search with the given taxon name(s). — is_datelife_result_empty","text":"","code":"is_datelife_result_empty(datelife_result, use_tnrs = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/is_datelife_result_empty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if we obtained an empty search with the given taxon name(s). — is_datelife_result_empty","text":"datelife_result datelifeResult object, usually output get_datelife_result(). use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names().","code":""},{"path":"http://phylotastic.org/datelife/reference/is_datelife_result_empty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if we obtained an empty search with the given taxon name(s). — is_datelife_result_empty","text":"Boolean. TRUE, chronograms found given taxon name(s). FALSE, chronogram search successful.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_good_chronogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a tree is a valid chronogram. — is_good_chronogram","title":"Check if a tree is a valid chronogram. — is_good_chronogram","text":"Check tree valid chronogram.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_good_chronogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a tree is a valid chronogram. — is_good_chronogram","text":"","code":"is_good_chronogram(phy)"},{"path":"http://phylotastic.org/datelife/reference/is_good_chronogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a tree is a valid chronogram. — is_good_chronogram","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_good_chronogram.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a tree is a valid chronogram. — is_good_chronogram","text":"TRUE valid tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/is_n_overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","title":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","text":"function implements definition 2.8 n-overlap Ané et al. (2009) doi:10.1007/s00026-009-0017-x .","code":""},{"path":"http://phylotastic.org/datelife/reference/is_n_overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","text":"","code":"is_n_overlap(names_1, names_2, n = 2)"},{"path":"http://phylotastic.org/datelife/reference/is_n_overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","text":"names_1 First vector names names_2 Second vector names n Degree overlap required","code":""},{"path":"http://phylotastic.org/datelife/reference/is_n_overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","text":"Boolean whether degree overlap met .","code":""},{"path":"http://phylotastic.org/datelife/reference/is_n_overlap.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap — is_n_overlap","text":"Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). \"Groves phylogenetic trees\". Annals Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x .","code":""},{"path":"http://phylotastic.org/datelife/reference/make_all_associations.html","id":null,"dir":"Reference","previous_headings":"","what":"Find all authors and where they have deposited their trees — make_all_associations","title":"Find all authors and where they have deposited their trees — make_all_associations","text":"Find authors deposited trees","code":""},{"path":"http://phylotastic.org/datelife/reference/make_all_associations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find all authors and where they have deposited their trees — make_all_associations","text":"","code":"make_all_associations(outputfile = \"depositorcache.RData\")"},{"path":"http://phylotastic.org/datelife/reference/make_all_associations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find all authors and where they have deposited their trees — make_all_associations","text":"outputfile Path including file name. NULL prevent saving.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_all_associations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find all authors and where they have deposited their trees — make_all_associations","text":"data.frame \"person\" \"urls\".","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bladj_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","title":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","text":"function takes tree topology uses BLADJ algorithm implemented phylocomr::ph_bladj() assign node ages branch lengths, given set fixed node ages respective node names.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bladj_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","text":"","code":"make_bladj_tree(tree = NULL, nodenames = NULL, nodeages = NULL)"},{"path":"http://phylotastic.org/datelife/reference/make_bladj_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","text":"tree tree either newick character string phylo object. nodenames character vector names nodes tree known ages nodeages numeric vector actual ages named nodes","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bladj_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bladj_tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. — make_bladj_tree","text":"Input tree can dated , $edge.length ignored. Ages given nodeages fixed corresponding nodes given nodenames.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bold_otol_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","title":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","text":"make_bold_otol_tree takes taxon names tree topology vector names search genetic markers Barcode Life Database (BOLD), create alignment, reconstruct branch lengths tree topology Maximum Likelihood.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bold_otol_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","text":"","code":"make_bold_otol_tree( input = c(\"Rhea americana\", \"Struthio camelus\", \"Gallus gallus\"), marker = \"COI\", otol_version = \"v3\", chronogram = TRUE, doML = FALSE, aligner = \"muscle\", ... )"},{"path":"http://phylotastic.org/datelife/reference/make_bold_otol_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","text":"input One following: character vector taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. datelifeQuery object output make_datelife_query(). marker character vector indicating gene BOLD system used branch length estimation. otol_version Version Open Tree Life use chronogram Default TRUE, branch lengths returned estimated ape::chronoMPL(). FALSE, branch lengths returned estimated phangorn::acctran() represent relative substitution rates. doML Default FALSE. TRUE, ML branch length optimization phangorn::optim.pml(). aligner character vector indicating whether use MAFFT MUSCLE align BOLD sequences. case sensitive. Default MUSCLE, supported using msa package Bioconductor, needs installed using BiocManager::install(). ... Arguments passed get_otol_synthetic_tree resolve Defaults TRUE. Whether resolve tree random . ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match().","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bold_otol_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","text":"phylo object. enough BOLD sequences available input taxon names, function returns tree branch lengths proportional relative substitution rate. enough BOLD sequences available input taxon names, function returns topology given input, synthetic Open Tree Life taxon names given input, obtained get_otol_synthetic_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/make_bold_otol_tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. — make_bold_otol_tree","text":"input phylo object newick string, used backbone topology. input character vector taxon names, induced synthetic OpenTree subtree used backbone.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_contributor_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a cache from Open Tree of Life — make_contributor_cache","title":"Create a cache from Open Tree of Life — make_contributor_cache","text":"Create cache Open Tree Life","code":""},{"path":"http://phylotastic.org/datelife/reference/make_contributor_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a cache from Open Tree of Life — make_contributor_cache","text":"","code":"make_contributor_cache(outputfile = \"contributorcache.RData\")"},{"path":"http://phylotastic.org/datelife/reference/make_contributor_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a cache from Open Tree of Life — make_contributor_cache","text":"outputfile Path including file name","code":""},{"path":"http://phylotastic.org/datelife/reference/make_contributor_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a cache from Open Tree of Life — make_contributor_cache","text":"List containing author curator results","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from taxon names to a datelifeQuery object — make_datelife_query","title":"Go from taxon names to a datelifeQuery object — make_datelife_query","text":"Go taxon names datelifeQuery object","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from taxon names to a datelifeQuery object — make_datelife_query","text":"","code":"make_datelife_query( input = c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), use_tnrs = TRUE, get_spp_from_taxon = FALSE, reference_taxonomy = \"ott\" )"},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from taxon names to a datelifeQuery object — make_datelife_query","text":"input Taxon names one following: character vector taxon names taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. use_tnrs Whether use Open Tree Life's Taxonomic Name Resolution Service (TNRS) process input taxon names. Default TRUE, corrects misspellings taxonomic name variations tnrs_match(), wrapper rotl::tnrs_match_names(). get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\".","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from taxon names to a datelifeQuery object — make_datelife_query","text":"datelifeQuery object, list three elements: $phy phylo object NA, input tree. $cleaned_names character vector cleaned taxon names. $ott_ids numeric vector OTT ids use_tnrs = TRUE, NULL use_tnrs = FALSE.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Go from taxon names to a datelifeQuery object — make_datelife_query","text":"processes phylo objects newick character string inputs input_process(). input multiPhylo object, first phylo element used. Similarly, input newick character string multiple trees, first one used.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query2.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from taxon names to a datelifeQuery object — make_datelife_query2","title":"Go from taxon names to a datelifeQuery object — make_datelife_query2","text":"Go taxon names datelifeQuery object","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from taxon names to a datelifeQuery object — make_datelife_query2","text":"","code":"make_datelife_query2( input = c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), get_spp_from_taxon = FALSE, reference_taxonomy = \"ott\", ... )"},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from taxon names to a datelifeQuery object — make_datelife_query2","text":"input Taxon names one following: character vector taxon names taxon names single comma separated starting concatenated c(). phylogenetic tree taxon names tip labels phylo multiPhylo object, newick character string. get_spp_from_taxon Whether search ages species belonging given taxon . Default FALSE. TRUE, must length input. input newick string clades converted phylo object, order get_spp_from_taxon match phy$tip.label. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\". ... Arguments passed rotl::tnrs_match_names context_name name taxonomic context searched (length-one character vector NULL). Must match (case sensitive) one values returned tnrs_contexts. Default \"life\". do_approximate_matching logical indicating whether perform approximate string (.k.. “fuzzy”) matching. Using FALSE greatly improve speed. Default, however, TRUE. ids vector ids use identifying names. assigned name names array. ids provided, ids names must identical length. include_suppressed Ordinarily, quasi-taxa, incertae sedis buckets non-OTUs, suppressed TNRS results. parameter true, quasi-taxa allowed possible TNRS results.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from taxon names to a datelifeQuery object — make_datelife_query2","text":"datelifeQuery object, list four elements: $input_names character vector input taxon names. $tnrs_names character vector taxon names processed TNRS. $ott_ids numeric vector OTT ids. $phy phylo object NA, input tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_datelife_query2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Go from taxon names to a datelifeQuery object — make_datelife_query2","text":"processes phylo objects newick character string inputs input_process(). input multiPhylo object, first phylo element used. Similarly, input newick character string multiple trees, first one used.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_runfile.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mrBayes run block file with a constraint topology and a set of node\ncalibrations and missing taxa — make_mrbayes_runfile","title":"Make a mrBayes run block file with a constraint topology and a set of node\ncalibrations and missing taxa — make_mrbayes_runfile","text":"Make mrBayes run block file constraint topology set node calibrations missing taxa","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_runfile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mrBayes run block file with a constraint topology and a set of node\ncalibrations and missing taxa — make_mrbayes_runfile","text":"","code":"make_mrbayes_runfile( constraint = NULL, taxa = NULL, ncalibration = NULL, missing_taxa = NULL, age_distribution = \"fixed\", root_calibration = FALSE, mrbayes_output_file = \"mrbayes_run.nexus\" )"},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_runfile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mrBayes run block file with a constraint topology and a set of node\ncalibrations and missing taxa — make_mrbayes_runfile","text":"constraint constraint tree: phylo object newick character string, without branch lengths. taxa character vector taxon names maintained tree ncalibration node calibrations: phylo object branch lengths proportional time; case nodes ncalibration used calibration points. Alternatively, list two elements: first character vector node names phy calibrate; second numeric vector corresponding ages use calibrations. missing_taxa tree, data frame vector enlisting missing taxa want include. tree Either phylo object newick character string. contains taxa want end, missing non missing. tree used hard constraint. data.frame contains two columns named \"taxon\" \"clade\". first one contains character vector missing taxon names. second one contains character numeric vector nodes constraint tree taxon assigned. character vector contains names missing taxa. added random constraint tree. age_distribution character string specifying type calibration. \"fixed\" \"uniform\" implemented now. fixed age given ncalibration used fixed age. lognormal age given ncalibration used mean age. standard deviation can provided. # still need add option. default, 95 CI sd used. uniform age given ncalibration used mean age. min_age = 0.9 * mean age, max_age = 1.1 * mean age. root_calibration Used set calibration root . Default FALSE. relevant ncalibration specified. mrbayes_output_file character vector specifying name mrBayes run file outputs (can specify directory ).","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_runfile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mrBayes run block file with a constraint topology and a set of node\ncalibrations and missing taxa — make_mrbayes_runfile","text":"MrBayes block run file nexus format.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Take a constraint tree and use mrBayes to get node ages and branch lengths\ngiven a set of node calibrations without any data. — make_mrbayes_tree","title":"Take a constraint tree and use mrBayes to get node ages and branch lengths\ngiven a set of node calibrations without any data. — make_mrbayes_tree","text":"Take constraint tree use mrBayes get node ages branch lengths given set node calibrations without data.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Take a constraint tree and use mrBayes to get node ages and branch lengths\ngiven a set of node calibrations without any data. — make_mrbayes_tree","text":"","code":"make_mrbayes_tree( constraint = NULL, taxa = NULL, ncalibration = NULL, missing_taxa = NULL, age_distribution = \"fixed\", root_calibration = FALSE, mrbayes_output_file = \"mrbayes_run.nexus\" )"},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Take a constraint tree and use mrBayes to get node ages and branch lengths\ngiven a set of node calibrations without any data. — make_mrbayes_tree","text":"constraint constraint tree: phylo object newick character string, without branch lengths. taxa character vector taxon names maintained tree ncalibration node calibrations: phylo object branch lengths proportional time; case nodes ncalibration used calibration points. Alternatively, list two elements: first character vector node names phy calibrate; second numeric vector corresponding ages use calibrations. missing_taxa tree, data frame vector enlisting missing taxa want include. tree Either phylo object newick character string. contains taxa want end, missing non missing. tree used hard constraint. data.frame contains two columns named \"taxon\" \"clade\". first one contains character vector missing taxon names. second one contains character numeric vector nodes constraint tree taxon assigned. character vector contains names missing taxa. added random constraint tree. age_distribution character string specifying type calibration. \"fixed\" \"uniform\" implemented now. fixed age given ncalibration used fixed age. lognormal age given ncalibration used mean age. standard deviation can provided. # still need add option. default, 95 CI sd used. uniform age given ncalibration used mean age. min_age = 0.9 * mean age, max_age = 1.1 * mean age. root_calibration Used set calibration root . Default FALSE. relevant ncalibration specified. mrbayes_output_file character vector specifying name mrBayes run file outputs (can specify directory ).","code":""},{"path":"http://phylotastic.org/datelife/reference/make_mrbayes_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Take a constraint tree and use mrBayes to get node ages and branch lengths\ngiven a set of node calibrations without any data. — make_mrbayes_tree","text":"phylo object branch lengths proportional time. saves mrBayes outputs working directory.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_otol_associations.html","id":null,"dir":"Reference","previous_headings":"","what":"Associate Open Tree of Life authors with studies — make_otol_associations","title":"Associate Open Tree of Life authors with studies — make_otol_associations","text":"Associate Open Tree Life authors studies","code":""},{"path":"http://phylotastic.org/datelife/reference/make_otol_associations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Associate Open Tree of Life authors with studies — make_otol_associations","text":"","code":"make_otol_associations()"},{"path":"http://phylotastic.org/datelife/reference/make_otol_associations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Associate Open Tree of Life authors with studies — make_otol_associations","text":"data.frame author last name, author first names, comma delimited URLs OToL studies","code":""},{"path":"http://phylotastic.org/datelife/reference/make_overlap_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an overlap table — make_overlap_table","title":"Create an overlap table — make_overlap_table","text":"Create overlap table","code":""},{"path":"http://phylotastic.org/datelife/reference/make_overlap_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an overlap table — make_overlap_table","text":"","code":"make_overlap_table(results_table)"},{"path":"http://phylotastic.org/datelife/reference/make_overlap_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an overlap table — make_overlap_table","text":"results_table \"author.results\" \"curator.results\" data.frame","code":""},{"path":"http://phylotastic.org/datelife/reference/make_overlap_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an overlap table — make_overlap_table","text":"data.frame information curators clades worked ","code":""},{"path":"http://phylotastic.org/datelife/reference/make_sdm.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","title":"Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"Make Super Distance Matrix (SDM) list good matrices obtained get_goodmatrices()","code":""},{"path":"http://phylotastic.org/datelife/reference/make_sdm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"","code":"make_sdm(unpadded.matrices, weighting = \"flat\")"},{"path":"http://phylotastic.org/datelife/reference/make_sdm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"unpadded.matrices list patristic matrices, datelifeResult object. weighting character vector indicating much weight give tree input SDM analysis. Options : weighting = \"flat\" trees equal weighting. weighting = \"taxa\" Weight proportional number taxa. weighting = \"inverse\" Weight proportional 1 / number taxa. Defaults weighting = \"flat\".","code":""},{"path":"http://phylotastic.org/datelife/reference/make_sdm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices() — make_sdm","text":"matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/make_treebase_associations.html","id":null,"dir":"Reference","previous_headings":"","what":"Associate TreeBase authors with studies — make_treebase_associations","title":"Associate TreeBase authors with studies — make_treebase_associations","text":"Associate TreeBase authors studies","code":""},{"path":"http://phylotastic.org/datelife/reference/make_treebase_associations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Associate TreeBase authors with studies — make_treebase_associations","text":"","code":"make_treebase_associations()"},{"path":"http://phylotastic.org/datelife/reference/make_treebase_associations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Associate TreeBase authors with studies — make_treebase_associations","text":"data.frame author last name, author first names, comma delimited URLs TreeBase studies","code":""},{"path":"http://phylotastic.org/datelife/reference/make_treebase_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a cache from TreeBase — make_treebase_cache","title":"Create a cache from TreeBase — make_treebase_cache","text":"Create cache TreeBase","code":""},{"path":"http://phylotastic.org/datelife/reference/make_treebase_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a cache from TreeBase — make_treebase_cache","text":"","code":"make_treebase_cache(outputfile = \"treebasecache.RData\")"},{"path":"http://phylotastic.org/datelife/reference/make_treebase_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a cache from TreeBase — make_treebase_cache","text":"outputfile Path including file name","code":""},{"path":"http://phylotastic.org/datelife/reference/make_treebase_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a cache from TreeBase — make_treebase_cache","text":"List containing author curator results","code":""},{"path":"http://phylotastic.org/datelife/reference/map_nodes_ott.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","title":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","text":"Add Open Tree Life Taxonomy tree nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/map_nodes_ott.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","text":"","code":"map_nodes_ott(tree)"},{"path":"http://phylotastic.org/datelife/reference/map_nodes_ott.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","text":"tree tree either newick character string phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/map_nodes_ott.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","text":"phylo object \"nodelabels\".","code":""},{"path":"http://phylotastic.org/datelife/reference/map_nodes_ott.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Open Tree of Life Taxonomy to tree nodes. — map_nodes_ott","text":"","code":"if (FALSE) # This is a flag for package development. You are welcome to run the example. # Load the Open Tree chronograms database cached in datelife: utils::data(opentree_chronograms) # Get the small chronograms (i.e., chronograms with less that ten tips) to generate a pretty plot: small <- opentree_chronograms$trees[unlist(sapply(opentree_chronograms$trees, ape::Ntip)) < 10] # Now, map the Open Tree taxonomy to the nodes of the first tree phy <- map_nodes_ott(tree = small[[1]]) # and plot it: # plot_phylo_all(phy) library(ape) plot(phy) nodelabels(phy$node.label) #end dontrun"},{"path":"http://phylotastic.org/datelife/reference/match_all_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Match calibrations to nodes of a given tree — match_all_calibrations","title":"Match calibrations to nodes of a given tree — match_all_calibrations","text":"match_all_calibrations searches given tree recent common ancestor (mrca) taxon name pairs datelifeCalibration. uses phytools::findMRCA().","code":""},{"path":"http://phylotastic.org/datelife/reference/match_all_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match calibrations to nodes of a given tree — match_all_calibrations","text":"","code":"match_all_calibrations(phy, calibrations)"},{"path":"http://phylotastic.org/datelife/reference/match_all_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match calibrations to nodes of a given tree — match_all_calibrations","text":"phy phylo object. calibrations calibrations object, output extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/match_all_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match calibrations to nodes of a given tree — match_all_calibrations","text":"list two elements: phy phylo object nodes renamed tree_add_nodelabels(). matched_calibrations matchedCalibrations object, input calibrations object two additional columns storing results mrca search phytools::findMRCA(): $mrca_node_number $mrca_node_name.","code":""},{"path":"http://phylotastic.org/datelife/reference/match_all_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Match calibrations to nodes of a given tree — match_all_calibrations","text":"function takes pairs taxon names secondary calibrations data frame, looks vector tip labels tree. present, gets node represents recent common ancestor (mrca) pair taxa tree. Nodes input phy can named .","code":""},{"path":"http://phylotastic.org/datelife/reference/matrices_to_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from a list of patristic distance matrix to a table of node ages — matrices_to_table","title":"Go from a list of patristic distance matrix to a table of node ages — matrices_to_table","text":"Go list patristic distance matrix table node ages","code":""},{"path":"http://phylotastic.org/datelife/reference/matrices_to_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from a list of patristic distance matrix to a table of node ages — matrices_to_table","text":"","code":"matrices_to_table(matrices)"},{"path":"http://phylotastic.org/datelife/reference/matrices_to_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from a list of patristic distance matrix to a table of node ages — matrices_to_table","text":"matrices names list patristic distance matrices. Names correspond study reference.","code":""},{"path":"http://phylotastic.org/datelife/reference/matrices_to_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from a list of patristic distance matrix to a table of node ages — matrices_to_table","text":"single data.frame \"taxonA\", \"taxonB\", \"age\".","code":""},{"path":"http://phylotastic.org/datelife/reference/matrix_to_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from a patristic distance matrix to a node ages table — matrix_to_table","title":"Go from a patristic distance matrix to a node ages table — matrix_to_table","text":"Go patristic distance matrix node ages table","code":""},{"path":"http://phylotastic.org/datelife/reference/matrix_to_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from a patristic distance matrix to a node ages table — matrix_to_table","text":"","code":"matrix_to_table(matrix, reference)"},{"path":"http://phylotastic.org/datelife/reference/matrix_to_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from a patristic distance matrix to a node ages table — matrix_to_table","text":"matrix patristic distance matrix. reference character vector study reference ages come .","code":""},{"path":"http://phylotastic.org/datelife/reference/matrix_to_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from a patristic distance matrix to a node ages table — matrix_to_table","text":"data.frame \"taxonA\", \"taxonB\", \"age\".","code":""},{"path":"http://phylotastic.org/datelife/reference/message_multiphylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Message for a multiPhylo input — message_multiphylo","title":"Message for a multiPhylo input — message_multiphylo","text":"Message multiPhylo input","code":""},{"path":"http://phylotastic.org/datelife/reference/message_multiphylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Message for a multiPhylo input — message_multiphylo","text":"","code":"message_multiphylo()"},{"path":"http://phylotastic.org/datelife/reference/message_multiphylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Message for a multiPhylo input — message_multiphylo","text":"relevant message character string.","code":""},{"path":"http://phylotastic.org/datelife/reference/missing_taxa_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. — missing_taxa_check","title":"Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. — missing_taxa_check","text":"Checks missing_taxa argument ok used make_mrbayes_runfile inside tree_add_dates functions.","code":""},{"path":"http://phylotastic.org/datelife/reference/missing_taxa_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. — missing_taxa_check","text":"","code":"missing_taxa_check(missing_taxa = NULL, dated_tree = NULL)"},{"path":"http://phylotastic.org/datelife/reference/missing_taxa_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. — missing_taxa_check","text":"missing_taxa tree, data frame vector enlisting missing taxa want include. tree Either phylo object newick character string. contains taxa want end, missing non missing. tree used hard constraint. data.frame contains two columns named \"taxon\" \"clade\". first one contains character vector missing taxon names. second one contains character numeric vector nodes constraint tree taxon assigned. character vector contains names missing taxa. added random constraint tree. dated_tree tree (newick phylo) branch lengths proportional absolute time","code":""},{"path":"http://phylotastic.org/datelife/reference/missing_taxa_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. — missing_taxa_check","text":"phylo object, newick character string dataframe taxonomic assignations","code":""},{"path":"http://phylotastic.org/datelife/reference/mrca_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","title":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","text":"mrca_calibrations get nodes tree topology given phy correspond recent common ancestor (mrca) taxon pairs given calibrations. uses phytools::findMRCA() get mrca nodes.","code":""},{"path":"http://phylotastic.org/datelife/reference/mrca_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","text":"","code":"mrca_calibrations(phy, calibrations)"},{"path":"http://phylotastic.org/datelife/reference/mrca_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","text":"phy phylo object. calibrations calibrations object, output extract_calibrations_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/mrca_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","text":"list two elements: matched_phy phylo object nodes renamed match results mrca search. Nodes renamed using tree_add_nodelabels(). matched_calibrations matchedCalibrations object, input calibrations object two additional columns storing results mrca search phytools::findMRCA(): $mrca_node_number $mrca_node_name.","code":""},{"path":"http://phylotastic.org/datelife/reference/mrca_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Identify nodes of a tree topology that are most recent common ancestor (mrca)\nof taxon pairs from a calibrations object — mrca_calibrations","text":"function takes pairs taxon names calibrations data frame, looks vector tip labels tree. present, gets node represents recent common ancestor (mrca) pair taxa tree. Nodes input phy can named . renamed.","code":""},{"path":"http://phylotastic.org/datelife/reference/opentree_chronograms.html","id":null,"dir":"Reference","previous_headings":"","what":"Chronogram database — opentree_chronograms","title":"Chronogram database — opentree_chronograms","text":"Now storing >200 chronograms Open Tree Life","code":""},{"path":"http://phylotastic.org/datelife/reference/opentree_chronograms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Chronogram database — opentree_chronograms","text":"","code":"opentree_chronograms"},{"path":"http://phylotastic.org/datelife/reference/opentree_chronograms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Chronogram database — opentree_chronograms","text":"list four elements, containing data Open Tree Life chronograms authors list lists author names original studies published chronograms Open Tree Life database. curators list lists curator names uploaded chronograms Open Tree Life database. studies list study identifiers. trees multiPhylo object storing chronograms Open Tree Life database. update character vector indicating time database object last updated. version character vector indicating datelife utils::packageVersion() database last updated.","code":""},{"path":"http://phylotastic.org/datelife/reference/opentree_chronograms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Chronogram database — opentree_chronograms","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/opentree_chronograms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Chronogram database — opentree_chronograms","text":"Generated opentree_chronograms <- get_opentree_chronograms() opentree_chronograms$version <- '2023.12.30' usethis::use_data(opentree_chronograms, overwrite = T, compress = \"xz\") updated update_datelife_cache()","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_MRCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Get time of MRCA from patristic matrix. Used in datelife_result_MRCA(). — patristic_matrix_MRCA","title":"Get time of MRCA from patristic matrix. Used in datelife_result_MRCA(). — patristic_matrix_MRCA","text":"Get time MRCA patristic matrix. Used datelife_result_MRCA().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_MRCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get time of MRCA from patristic matrix. Used in datelife_result_MRCA(). — patristic_matrix_MRCA","text":"","code":"patristic_matrix_MRCA(patristic_matrix, na_rm = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_MRCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get time of MRCA from patristic matrix. Used in datelife_result_MRCA(). — patristic_matrix_MRCA","text":"patristic_matrix patristic matrix (aka datelifeResult object length 1) na_rm TRUE, drops rows containing NAs datelifeResult patristic matrix; FALSE, returns NA missing entries.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_MRCA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get time of MRCA from patristic matrix. Used in datelife_result_MRCA(). — patristic_matrix_MRCA","text":"depth MRCA numeric vector.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_congruify.html","id":null,"dir":"Reference","previous_headings":"","what":"patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. — patristic_matrix_array_congruify","title":"patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. — patristic_matrix_array_congruify","text":"patristic_matrix_array_congruify used patristic_matrix_array_subset_both patristic_matrix_array_congruify.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_congruify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. — patristic_matrix_array_congruify","text":"","code":"patristic_matrix_array_congruify( patristic_matrix_array, taxa, phy = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_congruify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. — patristic_matrix_array_congruify","text":"patristic_matrix_array patristic matrix array, rownames colnames must taxa. taxa Vector taxon names get subset . phy user tree congruify phylo object (ape). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_congruify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. — patristic_matrix_array_congruify","text":"patristic matrix ages target taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_phylo_congruify.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify a patristic matrix array from a given phylo object. — patristic_matrix_array_phylo_congruify","title":"Congruify a patristic matrix array from a given phylo object. — patristic_matrix_array_phylo_congruify","text":"Congruify patristic matrix array given phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_phylo_congruify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify a patristic matrix array from a given phylo object. — patristic_matrix_array_phylo_congruify","text":"","code":"patristic_matrix_array_phylo_congruify( patristic_matrix, target_tree, dating_method = \"PATHd8\", attempt_fix = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_phylo_congruify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify a patristic matrix array from a given phylo object. — patristic_matrix_array_phylo_congruify","text":"patristic_matrix patristic matrix, rownames colnames must taxa. target_tree phylo object. Use case want specific backbone output tree. dating_method method used tree dating. attempt_fix Default TRUE. congruification results NA branch lengths, attempt fix .","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_phylo_congruify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify a patristic matrix array from a given phylo object. — patristic_matrix_array_phylo_congruify","text":"matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a patristic matrix array\nUsed inside: patristic_matrix_array_congruify — patristic_matrix_array_split","title":"Split a patristic matrix array\nUsed inside: patristic_matrix_array_congruify — patristic_matrix_array_split","text":"Split patristic matrix array Used inside: patristic_matrix_array_congruify","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a patristic matrix array\nUsed inside: patristic_matrix_array_congruify — patristic_matrix_array_split","text":"","code":"patristic_matrix_array_split(patristic_matrix_array)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a patristic matrix array\nUsed inside: patristic_matrix_array_congruify — patristic_matrix_array_split","text":"patristic_matrix_array patristic matrix array, rownames colnames must taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a patristic matrix array\nUsed inside: patristic_matrix_array_congruify — patristic_matrix_array_split","text":"patristic matrix 3d array.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset a patristic matrix array — patristic_matrix_array_subset","title":"Subset a patristic matrix array — patristic_matrix_array_subset","text":"Subset patristic matrix array","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset a patristic matrix array — patristic_matrix_array_subset","text":"","code":"patristic_matrix_array_subset(patristic_matrix_array, taxa, phy4 = NULL)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a patristic matrix array — patristic_matrix_array_subset","text":"patristic_matrix_array patristic matrix array, rownames colnames must taxa. taxa Vector taxon names get subset . phy4 user tree congruify phylo4 format (phylobase).","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a patristic matrix array — patristic_matrix_array_subset","text":"list patristic matrix array $problem .","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset_both.html","id":null,"dir":"Reference","previous_headings":"","what":"Are all desired taxa in the patristic matrix array? — patristic_matrix_array_subset_both","title":"Are all desired taxa in the patristic matrix array? — patristic_matrix_array_subset_both","text":"patristic_matrix_array_subset_both used inside get_subset_array_dispatch().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset_both.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Are all desired taxa in the patristic matrix array? — patristic_matrix_array_subset_both","text":"","code":"patristic_matrix_array_subset_both( patristic_matrix_array, taxa, phy = NULL, phy4 = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset_both.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Are all desired taxa in the patristic matrix array? — patristic_matrix_array_subset_both","text":"patristic_matrix_array patristic matrix array, rownames colnames must taxa. taxa Vector taxon names get subset . phy user tree congruify phylo object (ape). phy4 user tree congruify phylo4 format (phylobase). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_array_subset_both.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Are all desired taxa in the patristic matrix array? — patristic_matrix_array_subset_both","text":"patristic matrix ages target taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_list_to_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert list of patristic matrices to a 3D array. — patristic_matrix_list_to_array","title":"Convert list of patristic matrices to a 3D array. — patristic_matrix_list_to_array","text":"patristic_matrix_list_to_array us ised inside summarize_datelife_result(), patristic_matrix_array_congruify().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_list_to_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert list of patristic matrices to a 3D array. — patristic_matrix_list_to_array","text":"","code":"patristic_matrix_list_to_array(patristic_matrix_list, pad = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_list_to_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert list of patristic matrices to a 3D array. — patristic_matrix_list_to_array","text":"patristic_matrix_list List patristic matrices pad TRUE, pad missing entries","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_list_to_array.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert list of patristic matrices to a 3D array. — patristic_matrix_list_to_array","text":"3d array patristic matrices","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_order_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Test the name order of a patristic matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_order_test","title":"Test the name order of a patristic matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_order_test","text":"patristic_matrix_name_order_test used patristic_matrix_list_to_array().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_order_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test the name order of a patristic matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_order_test","text":"","code":"patristic_matrix_name_order_test( patristic_matrix, standard.rownames, standard.colnames )"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_order_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test the name order of a patristic matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_order_test","text":"patristic_matrix patristic matrix, rownames colnames must taxa. standard.rownames character vector row names. standard.colnames character vector column names.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_order_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test the name order of a patristic matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_order_test","text":"Boolean.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_reorder.html","id":null,"dir":"Reference","previous_headings":"","what":"Reorder a matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_reorder","title":"Reorder a matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_reorder","text":"patristic_matrix_name_reorder used : patristic_matrix_pad().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_reorder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reorder a matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_reorder","text":"","code":"patristic_matrix_name_reorder(patristic_matrix)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_reorder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reorder a matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_reorder","text":"patristic_matrix patristic matrix, rownames colnames must taxa.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_name_reorder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reorder a matrix so that row and column labels are in alphabetical order. — patristic_matrix_name_reorder","text":"patristic matrix row column names taxa alphabetical order.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_pad.html","id":null,"dir":"Reference","previous_headings":"","what":"Fill in empty cells in a patristic matrix for missing taxa. — patristic_matrix_pad","title":"Fill in empty cells in a patristic matrix for missing taxa. — patristic_matrix_pad","text":"Used : patristic_matrix_list_to_array().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_pad.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fill in empty cells in a patristic matrix for missing taxa. — patristic_matrix_pad","text":"","code":"patristic_matrix_pad(patristic_matrix, all_taxa)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_pad.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fill in empty cells in a patristic matrix for missing taxa. — patristic_matrix_pad","text":"patristic_matrix patristic matrix, rownames colnames must taxa. all_taxa vector names taxa want, including ones patristic matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_pad.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fill in empty cells in a patristic matrix for missing taxa. — patristic_matrix_pad","text":"patristic matrix, NA entries taxa least one original patristic matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_taxa_all_matching.html","id":null,"dir":"Reference","previous_headings":"","what":"Are all desired taxa in the patristic matrix? — patristic_matrix_taxa_all_matching","title":"Are all desired taxa in the patristic matrix? — patristic_matrix_taxa_all_matching","text":"patristic_matrix_taxa_all_matching used inside: results_list_process().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_taxa_all_matching.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Are all desired taxa in the patristic matrix? — patristic_matrix_taxa_all_matching","text":"","code":"patristic_matrix_taxa_all_matching(patristic_matrix, taxa)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_taxa_all_matching.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Are all desired taxa in the patristic matrix? — patristic_matrix_taxa_all_matching","text":"patristic_matrix patristic matrix, rownames colnames must taxa. taxa Vector taxon names get subset .","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_taxa_all_matching.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Are all desired taxa in the patristic matrix? — patristic_matrix_taxa_all_matching","text":"Boolean.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_newick.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. — patristic_matrix_to_newick","title":"Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. — patristic_matrix_to_newick","text":"Convert patristic matrix newick string. Used inside: summarize_datelife_result.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_newick.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. — patristic_matrix_to_newick","text":"","code":"patristic_matrix_to_newick(patristic_matrix)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_newick.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. — patristic_matrix_to_newick","text":"patristic_matrix patristic matrix","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_newick.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. — patristic_matrix_to_newick","text":"newick string","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","title":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","text":"Function patristic_matrix_to_phylo used inside summarize_datelife_result().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","text":"","code":"patristic_matrix_to_phylo( patristic_matrix, clustering_method = \"nj\", fix_negative_brlen = TRUE, fixing_method = 0, ultrametric = TRUE, variance_matrix = NULL )"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","text":"patristic_matrix patristic matrix clustering_method character vector indicating method construct tree. Options : nj Neighbor-Joining method applied ape::nj(). upgma Unweighted Pair Group Method Arithmetic Mean method applied phangorn::upgma(). bionj improved version Neighbor-Joining method applied ape::bionj(). triangle Triangles method applied ape::triangMtd() mvr Minimum Variance Reduction method applied ape::mvr(). fix_negative_brlen Boolean indicating whether fix negative branch lengths resulting tree . Default TRUE. fixing_method character vector specifying method fix branch lengths: \"bladj\", \"mrbayes\" number assigned branches meeting fixing_criterion ultrametric Boolean indicating whether force ultrametric . variance_matrix variance matrix datelifeResult object, usually output datelife_result_variance_matrix(). used clustering_method = \"mvr\".","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","text":"rooted phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_to_phylo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert a patristic matrix to a phylo object. — patristic_matrix_to_phylo","text":"might add option insert function clustering_method future. , hard-coded function try Neighbor-Joining (NJ) first; errors, try UPGMA. Now, uses NJ \"phylo_all\" summary, using algorithm get tree summary matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_unpad.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to remove missing taxa from a datelifeResult object. — patristic_matrix_unpad","title":"Function to remove missing taxa from a datelifeResult object. — patristic_matrix_unpad","text":"Used datelife_result_sdm_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_unpad.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to remove missing taxa from a datelifeResult object. — patristic_matrix_unpad","text":"","code":"patristic_matrix_unpad(patristic_matrix)"},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_unpad.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to remove missing taxa from a datelifeResult object. — patristic_matrix_unpad","text":"patristic_matrix patristic matrix row column names taxa","code":""},{"path":"http://phylotastic.org/datelife/reference/patristic_matrix_unpad.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to remove missing taxa from a datelifeResult object. — patristic_matrix_unpad","text":"patristic_matrix all_taxa","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if phy is a phylo object and/or a chronogram. — phylo_check","title":"Checks if phy is a phylo object and/or a chronogram. — phylo_check","text":"Checks phy phylo object /chronogram.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if phy is a phylo object and/or a chronogram. — phylo_check","text":"","code":"phylo_check(phy = NULL, brlen = FALSE, dated = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/phylo_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if phy is a phylo object and/or a chronogram. — phylo_check","text":"phy phylo object. brlen Boolean. TRUE checks phylo object branch lengths. dated Boolean. TRUE checks phylo object ultrametric.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if phy is a phylo object and/or a chronogram. — phylo_check","text":"Nothing","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_congruify.html","id":null,"dir":"Reference","previous_headings":"","what":"Congruify a reference tree and a target tree given as phylo objects. — phylo_congruify","title":"Congruify a reference tree and a target tree given as phylo objects. — phylo_congruify","text":"Congruify reference tree target tree given phylo objects.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_congruify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Congruify a reference tree and a target tree given as phylo objects. — phylo_congruify","text":"","code":"phylo_congruify( reference_tree, target_tree, dating_method = \"PATHd8\", attempt_fix = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/phylo_congruify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Congruify a reference tree and a target tree given as phylo objects. — phylo_congruify","text":"reference_tree phylo object. target_tree phylo object. Use case want specific backbone output tree. dating_method method used tree dating. attempt_fix Default TRUE. congruification results NA branch lengths, attempt fix .","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_congruify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Congruify a reference tree and a target tree given as phylo objects. — phylo_congruify","text":"matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"Generate uncertainty branch lengths using lognormal.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"","code":"phylo_generate_uncertainty( phy, size = 100, uncertainty_method = \"other\", age_distribution = \"uniform\", age_sd = NULL, age_var = 0.1, age_scale = 0, alpha = 0.025, rescale = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"phy phylo object. size numeric vector indicating number samples generated. uncertainty_method character vector specifying method generate uncertainty. mrbayes default. age_distribution character string specifying type calibration. \"fixed\" \"uniform\" implemented now. fixed age given ncalibration used fixed age. lognormal age given ncalibration used mean age. standard deviation can provided. # still need add option. default, 95 CI sd used. uniform age given ncalibration used mean age. min_age = 0.9 * mean age, max_age = 1.1 * mean age. age_sd standard deviation around age use generating uncertainty. numeric value, var used calculate . age_var variance calculate age_sd generate uncertainty. age_scale scale sd depth node. 0, sd . , older nodes uncertainty alpha significance level uncertainty generate. default 0.025 rescale Boolean. true, observed age rescaled round.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"phylo multiPhylo object topology phy different branch lengths","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"want change size sampled trees need run mrbayes . Just use sample_trees(\"mrbayes_trees_file_directory\", size = new_size) get multiPhylo object new tree sample.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_generate_uncertainty.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate uncertainty in branch lengths using a lognormal. — phylo_generate_uncertainty","text":"","code":"if (FALSE) { # Generate uncertainty over feline species SDM chronogram. # Load the data: data(felid_sdm) # By default, generates a sample of 100 trees with var = 0.1: unc <- phylo_generate_uncertainty(felid_sdm$phy) length(unc) # Make an LTT plot: max_age <- max(sapply(unc, ape::branching.times)) ape::ltt.plot(phy = unc[[1]], xlim = c(-max_age, 0), col = \"#cce5ff50\") for (i in 2:100) { ape::ltt.lines(phy = unc[[i]], col = \"#cce5ff50\") } ape::ltt.lines(felid_sdm$phy, col = \"red\") title(c(\"fake uncertainty\", \"in Felidae SDM chronogram\")) } # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/phylo_get_node_numbers.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets node numbers from any phylogeny — phylo_get_node_numbers","title":"Gets node numbers from any phylogeny — phylo_get_node_numbers","text":"Gets node numbers phylogeny","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_node_numbers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets node numbers from any phylogeny — phylo_get_node_numbers","text":"","code":"phylo_get_node_numbers(phy)"},{"path":"http://phylotastic.org/datelife/reference/phylo_get_node_numbers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets node numbers from any phylogeny — phylo_get_node_numbers","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_node_numbers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets node numbers from any phylogeny — phylo_get_node_numbers","text":"numeric vector node numbers","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a subset array from a phylo object — phylo_get_subset_array","title":"Get a subset array from a phylo object — phylo_get_subset_array","text":"Get subset array phylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a subset array from a phylo object — phylo_get_subset_array","text":"","code":"phylo_get_subset_array( reference_tree, taxa, phy4 = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a subset array from a phylo object — phylo_get_subset_array","text":"reference_tree phylo object. taxa Vector taxon names get subset . phy4 user tree congruify phylo4 format (phylobase). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a subset array from a phylo object — phylo_get_subset_array","text":"list patristic matrix array $problem .","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array_congruify.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a congruified subset array from a phylo object — phylo_get_subset_array_congruify","title":"Get a congruified subset array from a phylo object — phylo_get_subset_array_congruify","text":"Get congruified subset array phylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array_congruify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a congruified subset array from a phylo object — phylo_get_subset_array_congruify","text":"","code":"phylo_get_subset_array_congruify( reference_tree, taxa, phy = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array_congruify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a congruified subset array from a phylo object — phylo_get_subset_array_congruify","text":"reference_tree phylo object. taxa Vector taxon names get subset . phy user tree congruify phylo object (ape). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_get_subset_array_congruify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a congruified subset array from a phylo object — phylo_get_subset_array_congruify","text":"list patristic matrix array $problem .","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_has_brlen.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a tree has branch lengths — phylo_has_brlen","title":"Check if a tree has branch lengths — phylo_has_brlen","text":"Check tree branch lengths","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_has_brlen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a tree has branch lengths — phylo_has_brlen","text":"","code":"phylo_has_brlen(phy)"},{"path":"http://phylotastic.org/datelife/reference/phylo_has_brlen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a tree has branch lengths — phylo_has_brlen","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_has_brlen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a tree has branch lengths — phylo_has_brlen","text":"TRUE FALSE","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_prune_missing_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Prune missing taxa from a phylo object\nUsed inside phylo_get_subset_array and phylo_get_subset_array_congruify. — phylo_prune_missing_taxa","title":"Prune missing taxa from a phylo object\nUsed inside phylo_get_subset_array and phylo_get_subset_array_congruify. — phylo_prune_missing_taxa","text":"Prune missing taxa phylo object Used inside phylo_get_subset_array phylo_get_subset_array_congruify.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_prune_missing_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prune missing taxa from a phylo object\nUsed inside phylo_get_subset_array and phylo_get_subset_array_congruify. — phylo_prune_missing_taxa","text":"","code":"phylo_prune_missing_taxa(phy, taxa)"},{"path":"http://phylotastic.org/datelife/reference/phylo_prune_missing_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prune missing taxa from a phylo object\nUsed inside phylo_get_subset_array and phylo_get_subset_array_congruify. — phylo_prune_missing_taxa","text":"phy user tree congruify phylo object (ape). taxa Vector taxon names get subset .","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_prune_missing_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prune missing taxa from a phylo object\nUsed inside phylo_get_subset_array and phylo_get_subset_array_congruify. — phylo_prune_missing_taxa","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_subset_both.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset a reference and a target tree given as phylo objects. — phylo_subset_both","title":"Subset a reference and a target tree given as phylo objects. — phylo_subset_both","text":"Subset reference target tree given phylo objects.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_subset_both.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset a reference and a target tree given as phylo objects. — phylo_subset_both","text":"","code":"phylo_subset_both( reference_tree, taxa, phy = NULL, phy4 = NULL, dating_method = \"PATHd8\" )"},{"path":"http://phylotastic.org/datelife/reference/phylo_subset_both.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a reference and a target tree given as phylo objects. — phylo_subset_both","text":"reference_tree phylo object. taxa Vector taxon names get subset . phy user tree congruify phylo object (ape). phy4 user tree congruify phylo4 format (phylobase). dating_method method used tree dating.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_subset_both.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a reference and a target tree given as phylo objects. — phylo_subset_both","text":"list patristic matrix array $problem .","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_space_to_underscore.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spaces to underscores in trees. — phylo_tiplabel_space_to_underscore","title":"Convert spaces to underscores in trees. — phylo_tiplabel_space_to_underscore","text":"phylo_tiplabel_space_to_underscore used : make_mrbayes_runfile(), tree_get_singleton_outgroup(), congruify_and_check(), patristic_matrix_array_phylo_congruify().","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_space_to_underscore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spaces to underscores in trees. — phylo_tiplabel_space_to_underscore","text":"","code":"phylo_tiplabel_space_to_underscore(phy)"},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_space_to_underscore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert spaces to underscores in trees. — phylo_tiplabel_space_to_underscore","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_space_to_underscore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spaces to underscores in trees. — phylo_tiplabel_space_to_underscore","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_underscore_to_space.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert underscores to spaces in trees. — phylo_tiplabel_underscore_to_space","title":"Convert underscores to spaces in trees. — phylo_tiplabel_underscore_to_space","text":"phylo_tiplabel_underscore_to_space used inside patristic_matrix_array_phylo_congruify(), congruify_and_check().","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_underscore_to_space.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert underscores to spaces in trees. — phylo_tiplabel_underscore_to_space","text":"","code":"phylo_tiplabel_underscore_to_space(phy)"},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_underscore_to_space.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert underscores to spaces in trees. — phylo_tiplabel_underscore_to_space","text":"phy phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_tiplabel_underscore_to_space.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert underscores to spaces in trees. — phylo_tiplabel_underscore_to_space","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_to_patristic_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a patristic matrix from a phylo object. — phylo_to_patristic_matrix","title":"Get a patristic matrix from a phylo object. — phylo_to_patristic_matrix","text":"Get patristic matrix phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_to_patristic_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a patristic matrix from a phylo object. — phylo_to_patristic_matrix","text":"","code":"phylo_to_patristic_matrix(phy, test = TRUE, tol = 0.01, option = 2)"},{"path":"http://phylotastic.org/datelife/reference/phylo_to_patristic_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a patristic matrix from a phylo object. — phylo_to_patristic_matrix","text":"phy phylo object. test Default TRUE. Whether test phy branch lengths ultrametric . tol branching time reference secondary constraints applied target option integer (1 2; see details).","code":""},{"path":"http://phylotastic.org/datelife/reference/phylo_to_patristic_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a patristic matrix from a phylo object. — phylo_to_patristic_matrix","text":"patristic matrix.","code":""},{"path":"http://phylotastic.org/datelife/reference/pick_grove.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick a grove in the case of multiple groves in a set of trees. — pick_grove","title":"Pick a grove in the case of multiple groves in a set of trees. — pick_grove","text":"Pick grove case multiple groves set trees.","code":""},{"path":"http://phylotastic.org/datelife/reference/pick_grove.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick a grove in the case of multiple groves in a set of trees. — pick_grove","text":"","code":"pick_grove(grove_list, criterion = \"taxa\", datelife_result)"},{"path":"http://phylotastic.org/datelife/reference/pick_grove.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick a grove in the case of multiple groves in a set of trees. — pick_grove","text":"grove_list list vectors tree indices. element grove. criterion Defaults criterion = \"taxa\". Used chronogram summarizing, .e., obtaining single summary chronogram group input chronograms. summarizing approaches return single summary tree group phylogenetic trees, necessary latter form grove, roughly, sufficiently overlapping set taxa trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x . rare cases, group trees can multiple groves. argument indicates whether get grove trees (criterion = \"trees\") taxa (criterion = \"taxa\"). datelife_result datelifeResult object. needed criterion = \"taxa\".","code":""},{"path":"http://phylotastic.org/datelife/reference/pick_grove.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pick a grove in the case of multiple groves in a set of trees. — pick_grove","text":"numeric vector elements picked grove.","code":""},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Some plants chronogram — plant_bold_otol_tree","title":"Some plants chronogram — plant_bold_otol_tree","text":"plants chronogram","code":""},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Some plants chronogram — plant_bold_otol_tree","text":"","code":"plant_bold_otol_tree"},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Some plants chronogram — plant_bold_otol_tree","text":"phylo object 6 tips 5 internal nodes edge Integer vector edge (branch) numbers tip.label Character vector species names plants Nnode Integer vector number nodes node.label Character vector node names edge.length Numeric vector edge (branch) lengths","code":""},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Some plants chronogram — plant_bold_otol_tree","text":"http://opentreeoflife.org http://www.boldsystems.org","code":""},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Some plants chronogram — plant_bold_otol_tree","text":"Generated make_bold_otol_tree(input = \"((Zea mays,Oryza sativa),((Arabidopsis thaliana,(Glycine max,Medicago sativa)),Solanum lycopersicum)Pentapetalae);\") usethis::use_data(plant_bold_otol_tree)","code":""},{"path":"http://phylotastic.org/datelife/reference/plant_bold_otol_tree.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Some plants chronogram — plant_bold_otol_tree","text":"Luna L. Sanchez-Reyes lsanche7@utk.edu Brian O'Meara bomeara@utk.edu","code":""},{"path":"http://phylotastic.org/datelife/reference/problems.html","id":null,"dir":"Reference","previous_headings":"","what":"Problematic chronograms from Open Tree of Life. — problems","title":"Problematic chronograms from Open Tree of Life. — problems","text":"Problematic chronograms Open Tree Life.","code":""},{"path":"http://phylotastic.org/datelife/reference/problems.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Problematic chronograms from Open Tree of Life. — problems","text":"","code":"problems"},{"path":"http://phylotastic.org/datelife/reference/problems.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Problematic chronograms from Open Tree of Life. — problems","text":"list trees unmapped taxa","code":""},{"path":"http://phylotastic.org/datelife/reference/problems.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Problematic chronograms from Open Tree of Life. — problems","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/problems.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Problematic chronograms from Open Tree of Life. — problems","text":"developed tools clean map tip labels cached trees found trees stored unmapped tip labels extracted saved used testing functions. Generated problems <- opentree_chronograms$trees[sapply(sapply(opentree_chronograms$trees, \"[\", \"tip.label\"), function(x) (grepl(\".mapped\", x)))] usethis::use_data(problems) opentree_chronograms object commit https://github.com/phylotastic/datelife/tree/be894448f6fc437241cd0916fab45e84ac3e09c6 [\", \"tip.label\"), function(x) (grepl(\".mapped\", x)))]: R:%22,%20%22tip.label%22),%20function(x)%20any(grepl(%22not.mapped%22,%20x)))","code":""},{"path":"http://phylotastic.org/datelife/reference/recover_mrcaott.html","id":null,"dir":"Reference","previous_headings":"","what":"Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id — recover_mrcaott","title":"Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id — recover_mrcaott","text":"Get mrcaott tag OpenTree induced synthetic tree get name ott id","code":""},{"path":"http://phylotastic.org/datelife/reference/recover_mrcaott.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id — recover_mrcaott","text":"","code":"recover_mrcaott(tag)"},{"path":"http://phylotastic.org/datelife/reference/recover_mrcaott.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id — recover_mrcaott","text":"tag character vector mrca tag","code":""},{"path":"http://phylotastic.org/datelife/reference/recover_mrcaott.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id — recover_mrcaott","text":"numeric vector ott id original taxon named corresponding ott name","code":""},{"path":"http://phylotastic.org/datelife/reference/relevant_curators_tabulate.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the relevant curators for a set of studies. — relevant_curators_tabulate","title":"Return the relevant curators for a set of studies. — relevant_curators_tabulate","text":"Return relevant curators set studies.","code":""},{"path":"http://phylotastic.org/datelife/reference/relevant_curators_tabulate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the relevant curators for a set of studies. — relevant_curators_tabulate","text":"","code":"relevant_curators_tabulate(results.index, cache = \"opentree_chronograms\")"},{"path":"http://phylotastic.org/datelife/reference/relevant_curators_tabulate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the relevant curators for a set of studies. — relevant_curators_tabulate","text":"results.index vector datelife_result_study_index() indices relevant studies. cache cached chronogram database.","code":""},{"path":"http://phylotastic.org/datelife/reference/relevant_curators_tabulate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the relevant curators for a set of studies. — relevant_curators_tabulate","text":"vector counts curator, names equal curator names.","code":""},{"path":"http://phylotastic.org/datelife/reference/results_list_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Take results_list and process it. — results_list_process","title":"Take results_list and process it. — results_list_process","text":"results_list_process used inside: get_datelife_result()","code":""},{"path":"http://phylotastic.org/datelife/reference/results_list_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Take results_list and process it. — results_list_process","text":"","code":"results_list_process(results_list, taxa = NULL, partial = FALSE)"},{"path":"http://phylotastic.org/datelife/reference/results_list_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Take results_list and process it. — results_list_process","text":"results_list list returned using get_subset_array_dispatch() opentree_chronograms$trees taxa Vector taxon names get subset . partial TRUE, return matrices partial matches.","code":""},{"path":"http://phylotastic.org/datelife/reference/results_list_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Take results_list and process it. — results_list_process","text":"list patristic.matrices NA.","code":""},{"path":"http://phylotastic.org/datelife/reference/run.html","id":null,"dir":"Reference","previous_headings":"","what":"Core function to generate results — run","title":"Core function to generate results — run","text":"Core function generate results","code":""},{"path":"http://phylotastic.org/datelife/reference/run.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Core function to generate results — run","text":"","code":"run( input = c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), format = \"citations\", partial = \"yes\", plot.width = 600, plot.height = 600, use_tnrs = \"no\", opentree_chronograms = NULL )"},{"path":"http://phylotastic.org/datelife/reference/run.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Core function to generate results — run","text":"input newick string vector taxa format output format partial deal trees subset taxa query plot.width Width pixels output plot plot.height Height pixels output plot use_tnrs Whether use OpenTree's TNRS input opentree_chronograms list lists containing input trees info","code":""},{"path":"http://phylotastic.org/datelife/reference/run.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Core function to generate results — run","text":"results desired format","code":""},{"path":"http://phylotastic.org/datelife/reference/run_mrbayes.html","id":null,"dir":"Reference","previous_headings":"","what":"Runs MrBayes from R — run_mrbayes","title":"Runs MrBayes from R — run_mrbayes","text":"Runs MrBayes R","code":""},{"path":"http://phylotastic.org/datelife/reference/run_mrbayes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runs MrBayes from R — run_mrbayes","text":"","code":"run_mrbayes(mrbayes_output_file = NULL)"},{"path":"http://phylotastic.org/datelife/reference/run_mrbayes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Runs MrBayes from R — run_mrbayes","text":"mrbayes_output_file character vector specifying name mrBayes run file outputs (can specify directory ).","code":""},{"path":"http://phylotastic.org/datelife/reference/run_mrbayes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Runs MrBayes from R — run_mrbayes","text":"phylo object consensus tree. MrBayes output files stored working directory.","code":""},{"path":"http://phylotastic.org/datelife/reference/sample_trees.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. — sample_trees","title":"Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. — sample_trees","text":"Sample trees file containing multiple trees. Usually bayesian analysis output trees file.","code":""},{"path":"http://phylotastic.org/datelife/reference/sample_trees.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. — sample_trees","text":"","code":"sample_trees(trees_file, trees_object = NULL, burnin = 0.25, size = 100)"},{"path":"http://phylotastic.org/datelife/reference/sample_trees.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. — sample_trees","text":"trees_file character vector indicating name directory file trees sample. trees_object R object containing list trees already read R tree file bayesian analysis output. burnin numeric vector indicating burnin fraction. number 0 1. Default 0.25 size numeric vector indicating number samples generated.","code":""},{"path":"http://phylotastic.org/datelife/reference/sample_trees.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. — sample_trees","text":"multiPhylo object random sample trees.","code":""},{"path":"http://phylotastic.org/datelife/reference/save_otol_chronograms.html","id":null,"dir":"Reference","previous_headings":"","what":"Save all chronograms from Open Tree of Life — save_otol_chronograms","title":"Save all chronograms from Open Tree of Life — save_otol_chronograms","text":"Save chronograms Open Tree Life","code":""},{"path":"http://phylotastic.org/datelife/reference/save_otol_chronograms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save all chronograms from Open Tree of Life — save_otol_chronograms","text":"","code":"save_otol_chronograms(file = \"opentree_chronograms.RData\")"},{"path":"http://phylotastic.org/datelife/reference/save_otol_chronograms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save all chronograms from Open Tree of Life — save_otol_chronograms","text":"file Path including file name","code":""},{"path":"http://phylotastic.org/datelife/reference/save_otol_chronograms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Save all chronograms from Open Tree of Life — save_otol_chronograms","text":"None","code":""},{"path":"http://phylotastic.org/datelife/reference/some_ants_datelife_result.html","id":null,"dir":"Reference","previous_headings":"","what":"datelifeResult object of some ants — some_ants_datelife_result","title":"datelifeResult object of some ants — some_ants_datelife_result","text":"datelifeResult object ants","code":""},{"path":"http://phylotastic.org/datelife/reference/some_ants_datelife_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"datelifeResult object of some ants — some_ants_datelife_result","text":"","code":"some_ants_datelife_result"},{"path":"http://phylotastic.org/datelife/reference/some_ants_datelife_result.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"datelifeResult object of some ants — some_ants_datelife_result","text":"list one element, containing named patristic matrix","code":""},{"path":"http://phylotastic.org/datelife/reference/some_ants_datelife_result.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"datelifeResult object of some ants — some_ants_datelife_result","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/some_ants_datelife_result.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"datelifeResult object of some ants — some_ants_datelife_result","text":"Generated : some_ants_input <- \"(Aulacopone_relicta,(((Myrmecia_gulosa,(Aneuretus_simoni,Dolichoderus_mariae)),((Ectatomma_ruidum,Huberia_brounii),Formica_rufa)),Apomyrma_stygia),Martialis_heureka)Formicidae;\" some_ants_datelife_query <- make_datelife_query(input = some_ants_input) some_ants_datelife_result <- get_datelife_result(input = some_ants_datelife_query) usethis::use_data(some_ants_datelife_result)","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_search.html","id":null,"dir":"Reference","previous_headings":"","what":"A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa — subset2_search","title":"A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa — subset2_search","text":"list datelifeQuery datelifeResult objects search taxon names subset2_taxa","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa — subset2_search","text":"","code":"subset2_search"},{"path":"http://phylotastic.org/datelife/reference/subset2_search.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa — subset2_search","text":"list two named elements. datelifeResult object 24 patristic matrices datelife_query datelifeQuery object using names_subset 2 input. datelife_result datelifeResult object resulting search names datelifeQuery","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_search.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa — subset2_search","text":"Generated : datelife_query <- make_datelife_query(subset2_taxa) datelife_result <- get_datelife_result(datelife_query) subset2_search <- list(query = datelife_query, result = datelife_result) usethis::use_data(subset2_search, overwrite = TRUE)","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","title":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","text":"Long list >2.7k virus, bacteria, plant animal taxon names","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","text":"","code":"subset2_taxa"},{"path":"http://phylotastic.org/datelife/reference/subset2_taxa.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","text":"character vector length 2778","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_taxa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","text":"https://github.com/phylotastic/rphylotastic/tree/master/tests/testthat","code":""},{"path":"http://phylotastic.org/datelife/reference/subset2_taxa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Long list of >2.7k virus, bacteria, plant and animal taxon names — subset2_taxa","text":"Generated : subset2_taxa <- rphylotastic::url_get_scientific_names(\"https://github.com/phylotastic/rphylotastic/blob/master/tests/testthat/subset2.txt\") usethis::use_data(subset2_taxa)","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_congruifiedCalibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get summary statistics of ages in a congruifiedCalibrations object. — summarize_congruifiedCalibrations","title":"Get summary statistics of ages in a congruifiedCalibrations object. — summarize_congruifiedCalibrations","text":"Function summarize_congruifiedCalibrations returns table summary statistics node congruified_calibrations argument.","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_congruifiedCalibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get summary statistics of ages in a congruifiedCalibrations object. — summarize_congruifiedCalibrations","text":"","code":"summarize_congruifiedCalibrations(congruified_calibrations, age_column)"},{"path":"http://phylotastic.org/datelife/reference/summarize_congruifiedCalibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get summary statistics of ages in a congruifiedCalibrations object. — summarize_congruifiedCalibrations","text":"congruified_calibrations congruifiedCalibrations object, output congruify_and_mrca_multiPhylo(). age_column character string indicating name column summarized.","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_congruifiedCalibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get summary statistics of ages in a congruifiedCalibrations object. — summarize_congruifiedCalibrations","text":"data.frame summarized ages.","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_datelife_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize a datelifeResult object. — summarize_datelife_result","title":"Summarize a datelifeResult object. — summarize_datelife_result","text":"Get different types summaries datelifeResult object, output get_datelife_result(). allows rapid processing data. need list chronograms datelifeResult object, function looking .","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_datelife_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize a datelifeResult object. — summarize_datelife_result","text":"","code":"summarize_datelife_result( datelife_result = NULL, datelife_query = NULL, summary_format = \"phylo_all\", na_rm = TRUE, summary_print = c(\"citations\", \"taxa\"), taxon_summary = c(\"none\", \"summary\", \"matrix\"), criterion = \"taxa\" )"},{"path":"http://phylotastic.org/datelife/reference/summarize_datelife_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize a datelifeResult object. — summarize_datelife_result","text":"datelife_result datelifeResult object, usually output get_datelife_result(). datelife_query datelifeQuery object, usually output make_datelife_query(). summary_format character vector length one, indicating output format results DateLife search. Available output formats : \"citations\" character vector references chronograms target taxa published (source chronograms). \"mrca\" named numeric vector recent common ancestor (mrca) ages target taxa defined input, obtained source chronograms. Names mrca vector equal citations. \"newick_all\" named character vector newick strings corresponding target chronograms derived source chronograms. Names newick_all vector equal citations. \"newick_sdm\" multiple source chronograms available. character vector single newick string corresponding target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"newick_median\" multiple source chronograms available. character vector single newick string corresponding target chronogram median source chronograms. \"phylo_sdm\" multiple source chronograms available. phylo object single target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"phylo_median\" multiple source chronograms available. phylo object single target chronogram obtained source chronograms median method. \"phylo_all\" named list phylo objects corresponding target chronogram obtained available source chronograms. Names phylo_all list correspond citations. \"phylo_biggest\" chronogram taxa. case tie, chronogram clade age closest median age equally large trees returned. \"html\" character vector html string can saved opened web browser. contains 4 column table data target taxa: mrca, number taxa, citations source chronogram newick target chronogram. \"data_frame\" 4 column data.frame data target taxa: mrca, number taxa, citations source chronograms newick string. na_rm TRUE, drops rows containing NAs datelifeResult patristic matrix; FALSE, returns NA missing entries. summary_print character vector specifying type summary information printed screen. Options : \"citations\" Prints references chronograms target taxa found. \"taxa\" Prints summary number chronograms target taxon found. \"none\" Nothing printed screen. Defaults c(\"citations\", \"taxa\"), displays . taxon_summary character vector specifying data target taxa missing source chronograms added output \"summary\" presence/absence \"matrix\". Default \"none\", information taxon_summary added output. criterion Defaults criterion = \"taxa\". Used chronogram summarizing, .e., obtaining single summary chronogram group input chronograms. summarizing approaches return single summary tree group phylogenetic trees, necessary latter form grove, roughly, sufficiently overlapping set taxa trees, see Ané et al. (2009) doi:10.1007/s00026-009-0017-x . rare cases, group trees can multiple groves. argument indicates whether get grove trees (criterion = \"trees\") taxa (criterion = \"taxa\").","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_datelife_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize a datelifeResult object. — summarize_datelife_result","text":"output determined argument summary_format: summary_format = \"citations\" function returns character vector references. summary_format = \"mrca\" function returns named numeric vector recent common ancestor (mrca) ages. summary_format = \"newick_[, sdm, median]\" function returns output chronograms newick strings. summary_format = \"phylo_[, sdm, median, biggest]\" function returns output chronograms phylo multiPhylo objects. summary_format = \"html\" \"data_frame\" function returns 4 column table data mrca ages, number taxa, references, output chronograms newick strings.","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_datelife_result.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Summarize a datelifeResult object. — summarize_datelife_result","text":"Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). \"Groves phylogenetic trees\". Annals Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x .","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_fossil_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize taxon age from PBDB to just a single min and max age — summarize_fossil_range","title":"Summarize taxon age from PBDB to just a single min and max age — summarize_fossil_range","text":"uses Paleobiology Database's API gather information ages specimens taxon. also look descendants taxon. fixes name misspellings possible. basically wrapper get_fossil_range.","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_fossil_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize taxon age from PBDB to just a single min and max age — summarize_fossil_range","text":"","code":"summarize_fossil_range(taxon, recent = FALSE, assume_recent_if_missing = TRUE)"},{"path":"http://phylotastic.org/datelife/reference/summarize_fossil_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize taxon age from PBDB to just a single min and max age — summarize_fossil_range","text":"taxon scientific name taxon want range occurrences recent TRUE, forces minimum age zero assume_recent_if_missing TRUE, taxon missing pbdb assumed recent","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_fossil_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize taxon age from PBDB to just a single min and max age — summarize_fossil_range","text":"single row data.frame max_ma min_ma specimens, rowname equal taxon input","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_summary_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets all ages per taxon pair from a distance matrix\nInternal function used in summary_matrix_to_phylo_all(). — summarize_summary_matrix","title":"Gets all ages per taxon pair from a distance matrix\nInternal function used in summary_matrix_to_phylo_all(). — summarize_summary_matrix","text":"Gets ages per taxon pair distance matrix Internal function used summary_matrix_to_phylo_all().","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_summary_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets all ages per taxon pair from a distance matrix\nInternal function used in summary_matrix_to_phylo_all(). — summarize_summary_matrix","text":"","code":"summarize_summary_matrix(summ_matrix)"},{"path":"http://phylotastic.org/datelife/reference/summarize_summary_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets all ages per taxon pair from a distance matrix\nInternal function used in summary_matrix_to_phylo_all(). — summarize_summary_matrix","text":"summ_matrix summary patristic distance matrix, ones obtained datelife_result_sdm_matrix() datelife_result_median_matrix().","code":""},{"path":"http://phylotastic.org/datelife/reference/summarize_summary_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets all ages per taxon pair from a distance matrix\nInternal function used in summary_matrix_to_phylo_all(). — summarize_summary_matrix","text":"data.frame pairwise ages, row number equal combinatory column names (row names), estimated ncol(summ_matrix)^2 - sum(1:(ncol(summ_matrix)-1)).","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.datelifeResult.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize a datelifeResult object. — summary.datelifeResult","title":"Summarize a datelifeResult object. — summary.datelifeResult","text":"Summarize datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.datelifeResult.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize a datelifeResult object. — summary.datelifeResult","text":"","code":"# S3 method for datelifeResult summary(object, datelife_query, na_rm = TRUE, ...)"},{"path":"http://phylotastic.org/datelife/reference/summary.datelifeResult.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize a datelifeResult object. — summary.datelifeResult","text":"object object class datelifeResult, usually output get_datelife_result(). datelife_query datelifeQuery object, usually output make_datelife_query(). na_rm Default TRUE, whether include partial matches . ... arguments passed methods.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.datelifeResult.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize a datelifeResult object. — summary.datelifeResult","text":"named list 11 elements: \"citations\" character vector references chronograms target taxa published (source chronograms). \"mrca\" named numeric vector recent common ancestor (mrca) ages target taxa defined input, obtained source chronograms. Names mrca vector equal citations. \"newick_all\" named character vector newick strings corresponding target chronograms derived source chronograms. Names newick_all vector equal citations. \"newick_sdm\" multiple source chronograms available. character vector single newick string corresponding target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"newick_median\" multiple source chronograms available. character vector single newick string corresponding target chronogram median source chronograms. \"phylo_sdm\" multiple source chronograms available. phylo object single target chronogram obtained SDM supertree method (Criscuolo et al. 2006). \"phylo_median\" multiple source chronograms available. phylo object single target chronogram obtained source chronograms median method. \"phylo_all\" named list phylo objects corresponding target chronogram obtained available source chronograms. Names phylo_all list correspond citations. \"phylo_biggest\" chronogram taxa. case tie, chronogram clade age closest median age equally large trees returned. \"html\" character vector html string can saved opened web browser. contains 4 column table data target taxa: mrca, number taxa, citations source chronogram newick target chronogram. \"data_frame\" 4 column data.frame data target taxa: mrca, number taxa, citations source chronograms newick string.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.matchedCalibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","title":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","text":"Summarize matchedCalibrations object summary.matchedCalibrations gets node age distribution matchedCalibrations object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.matchedCalibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","text":"","code":"# S3 method for matchedCalibrations summary(object, ...)"},{"path":"http://phylotastic.org/datelife/reference/summary.matchedCalibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","text":"object matchedCalibrations object, usually element output match_all_calibrations(). ... arguments passed methods.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.matchedCalibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","text":"summaryMatchedCalibrations object, list two matchedCalibrations objects: not_in_phy data.frame subset input matchedCalibrations object containing taxon name pairs present given tree. NULL input taxon names found given tree. in_phy data.frame subset input matchedCalibrations object containing taxon name pairs present given tree.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary.matchedCalibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize a matchedCalibrations object\nsummary.matchedCalibrations gets the node age distribution from a matchedCalibrations object. — summary.matchedCalibrations","text":"Columns in_phy$mrca_node_name in_phy$reference factors.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo.html","id":null,"dir":"Reference","previous_headings":"","what":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","title":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","text":"Go summary matrix ultrametric phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","text":"","code":"summary_matrix_to_phylo( summ_matrix, datelife_query = NULL, target_tree = NULL, total_distance = TRUE, use = \"mean\", ... )"},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","text":"summ_matrix summary patristic distance matrix, ones obtained datelife_result_sdm_matrix() datelife_result_median_matrix(). datelife_query datelifeQuery object, usually output make_datelife_query(). target_tree phylo object. Use case want specific backbone output tree. total_distance Whether input summ_matrix stores total age distance (tip tip) distance node tip. Default TRUE, divides matrix half, FALSE take . use character vector indicating type age use summary tree. One following: \"mean\" use mean() node ages summ_matrix. \"median\" uses stats::median() age node ages summ_matrix. \"min\" use min() age node ages summ_matrix. \"max\" Choose wanna conservative; use max() age node ages summ_matrix. \"midpoint\" use mean minimum age maximum age. ... Arguments passed summary_matrix_to_phylo_all","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","text":"ultrametric phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Go from a summary matrix to an ultrametric phylo object. — summary_matrix_to_phylo","text":"can take regular patristic distance matrix, simpler methods implemented patristic_matrix_to_phylo().","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","title":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","text":"Get minimum, median, mean, midpoint, maximum summary chronograms summary matrix datelifeResult object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","text":"","code":"summary_matrix_to_phylo_all( summ_matrix, datelife_query = NULL, target_tree = NULL, total_distance = TRUE, ... )"},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","text":"summ_matrix summary patristic distance matrix, ones obtained datelife_result_sdm_matrix() datelife_result_median_matrix(). datelife_query datelifeQuery object, usually output make_datelife_query(). target_tree phylo object. Use case want specific backbone output tree. total_distance Whether input summ_matrix stores total age distance (tip tip) distance node tip. Default TRUE, divides matrix half, FALSE take . ... Arguments passed get_otol_synthetic_tree otol_version Version Open Tree Life use resolve Defaults TRUE. Whether resolve tree random . input Optional. character vector names datelifeQuery object. ott_ids NULL, takes argument ignores input. numeric vector ott ids obtained rotl::taxonomy_taxon_info() rotl::tnrs_match_names() tnrs_match().","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","text":"multiPhylo object length 5. contains min, mean, median, midpoint, max summary chronograms.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_matrix_to_phylo_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get minimum, median, mean, midpoint, and maximum summary chronograms from a\nsummary matrix of a datelifeResult object. — summary_matrix_to_phylo_all","text":"function users can choose minimum, mean maximum ages summary matrix calibration points get single summary chronogram. Users get three summary chronograms multiPhylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_patristic_matrix_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. — summary_patristic_matrix_array","title":"Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. — summary_patristic_matrix_array","text":"Summarize patristic matrix array (default, median). Used inside: summarize_datelife_result.","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_patristic_matrix_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. — summary_patristic_matrix_array","text":"","code":"summary_patristic_matrix_array(patristic_matrix_array, fn = stats::median)"},{"path":"http://phylotastic.org/datelife/reference/summary_patristic_matrix_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. — summary_patristic_matrix_array","text":"patristic_matrix_array 3D array patristic matrices fn function use summarize","code":""},{"path":"http://phylotastic.org/datelife/reference/summary_patristic_matrix_array.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. — summary_patristic_matrix_array","text":"2d array median (max, mean, etc) input array","code":""},{"path":"http://phylotastic.org/datelife/reference/threebirds_dr.html","id":null,"dir":"Reference","previous_headings":"","what":"datelifeResult object of three birds ","title":"datelifeResult object of three birds ","text":"datelifeResult object three birds \"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"","code":""},{"path":"http://phylotastic.org/datelife/reference/threebirds_dr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"datelifeResult object of three birds ","text":"","code":"threebirds_dr"},{"path":"http://phylotastic.org/datelife/reference/threebirds_dr.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"datelifeResult object of three birds ","text":"list 9 named patristic matrix","code":""},{"path":"http://phylotastic.org/datelife/reference/threebirds_dr.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"datelifeResult object of three birds ","text":"http://opentreeoflife.org","code":""},{"path":"http://phylotastic.org/datelife/reference/threebirds_dr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"datelifeResult object of three birds ","text":"Generated : threebirds_dr <- get_datelife_result(input=c(\"Rhea americana\", \"Pterocnemia pennata\", \"Struthio camelus\"), partial = TRUE, use_tnrs = FALSE, approximate_match = TRUE, cache = \"opentree_chronograms\") use_data(threebirds_dr)","code":""},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":null,"dir":"Reference","previous_headings":"","what":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"Taxon name resolution service (tnrs) applied vector names batches","code":""},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"","code":"tnrs_match(input, reference_taxonomy, tip, ...) # S3 method for default tnrs_match(input, reference_taxonomy = \"ott\", ...) # S3 method for phylo tnrs_match(input, reference_taxonomy = \"ott\", tip = NULL, ...)"},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"input character vector taxon names, phylo object tip names, matched taxonomy. reference_taxonomy character vector specifying reference taxonomy use TNRS. Options \"ott\", \"ncbi\", \"gbif\" \"irmng\". function defaults \"ott\". tip vector mode numeric character specifying tips match. left empty tips matched. ... Arguments passed rotl::tnrs_match_names context_name name taxonomic context searched (length-one character vector NULL). Must match (case sensitive) one values returned tnrs_contexts. Default \"life\". do_approximate_matching logical indicating whether perform approximate string (.k.. “fuzzy”) matching. Using FALSE greatly improve speed. Default, however, TRUE. ids vector ids use identifying names. assigned name names array. ids provided, ids names must identical length. include_suppressed Ordinarily, quasi-taxa, incertae sedis buckets non-OTUs, suppressed TNRS results. parameter true, quasi-taxa allowed possible TNRS results.","code":""},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"object class data frame phylo, added class match_names. NULL NULL","code":""},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"limit number names can queried matched. output preserve elements original input phylo object add phy$mapped character vector indicating state mapping phy$tip.labels: phy$original.tip.label character vector preserving original labels. phy$ott_ids numeric vector ott id numbers matched tips. Unmatched original tips NaN. tips duplicated, tnrs run (avoiding increases function running time) result applied duplicated tip labels","code":""},{"path":"http://phylotastic.org/datelife/reference/tnrs_match.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Taxon name resolution service (tnrs) applied to a vector of names by batches — tnrs_match","text":"","code":"tnrs_match(input = c(\"Mus\")) #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================================================================| 100% #> search_string unique_name approximate_match score ott_id #> 1 mus Mus (genus in Deuterostomia) FALSE 1 1068778 #> is_synonym flags number_matches #> 1 FALSE SIBLING_HIGHER 3 tnrs_match(input = c(\"Mus\", \"Mus musculus\")) #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> search_string unique_name approximate_match score ott_id #> 1 mus Mus (genus in Deuterostomia) FALSE 1 1068778 #> 2 mus musculus Mus musculus FALSE 1 542509 #> is_synonym flags number_matches #> 1 FALSE SIBLING_HIGHER 3 #> 2 FALSE 1 tnrs_match(input = c(\"Mus\", \"Echinus\", \"Hommo\", \"Mus\")) #> ---> Runnning TNRS to match input names to reference taxonomy (OTT). #> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% #> search_string unique_name approximate_match score #> 1 mus Mus (genus in Deuterostomia) FALSE 1.00 #> 2 echinus Echinus (genus in Opisthokonta) FALSE 1.00 #> 3 hommo Homo TRUE 0.75 #> 1.1 mus Mus (genus in Deuterostomia) FALSE 1.00 #> ott_id is_synonym flags number_matches #> 1 1068778 FALSE SIBLING_HIGHER 3 #> 2 616574 FALSE sibling_higher 4 #> 3 770309 FALSE sibling_higher 1 #> 1.1 1068778 FALSE SIBLING_HIGHER 3"},{"path":"http://phylotastic.org/datelife/reference/tree_add_dates.html","id":null,"dir":"Reference","previous_headings":"","what":"Add missing taxa to a dated tree and fabricate node ages for these missing taxa. — tree_add_dates","title":"Add missing taxa to a dated tree and fabricate node ages for these missing taxa. — tree_add_dates","text":"function adds missing taxa chronogram given dated_tree. still work progress.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_dates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add missing taxa to a dated tree and fabricate node ages for these missing taxa. — tree_add_dates","text":"","code":"tree_add_dates( dated_tree = NULL, missing_taxa = NULL, dating_method = \"mrbayes\", adding_criterion = \"random\", mrbayes_output_file = \"mrbayes_tree_add_dates.nexus\" )"},{"path":"http://phylotastic.org/datelife/reference/tree_add_dates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add missing taxa to a dated tree and fabricate node ages for these missing taxa. — tree_add_dates","text":"dated_tree tree (newick phylo) branch lengths proportional absolute time missing_taxa tree, data frame vector enlisting missing taxa want include. tree Either phylo object newick character string. contains taxa want end, missing non missing. tree used hard constraint. data.frame contains two columns named \"taxon\" \"clade\". first one contains character vector missing taxon names. second one contains character numeric vector nodes constraint tree taxon assigned. character vector contains names missing taxa. added random constraint tree. dating_method method used tree dating, options \"mrbayes\" \"bladj\". adding_criterion used dating_method = \"mrbayes\". character vector specify missing_taxa added dated_tree. Choose one : adding_method = \"random\" missing_taxa added random dated_tree. adding_method = \"taxonomy\" taxa added dated_tree following dataframe taxonomic assignations given missing_taxa argument. dataframe given, OpenTree's reference taxonomy used. adding_method = \"tree\" taxa added dated_tree following tree given missing_taxa argument. tree given, OpenTree's synthetic tree used. mrbayes_output_file character vector specifying name mrBayes run file outputs (can specify directory ).","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_dates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add missing taxa to a dated tree and fabricate node ages for these missing taxa. — tree_add_dates","text":"phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_nodelabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds labels to nodes with no assigned label — tree_add_nodelabels","title":"Adds labels to nodes with no assigned label — tree_add_nodelabels","text":"Adds labels nodes assigned label","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_nodelabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds labels to nodes with no assigned label — tree_add_nodelabels","text":"","code":"tree_add_nodelabels(tree = NULL, node_prefix = \"n\", node_index = \"node_number\")"},{"path":"http://phylotastic.org/datelife/reference/tree_add_nodelabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds labels to nodes with no assigned label — tree_add_nodelabels","text":"tree tree either newick character string phylo object. node_prefix Character vector. length 1, used name nodes labels, followed number can node_number consecutive, specified node_index. node_index Character vector. Choose \"from_1\" \"node_number\" numeric index node labels. use consecutive numbers 1 total node number first case phylo node numbers second case (.e, Ntip + 1).","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_nodelabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds labels to nodes with no assigned label — tree_add_nodelabels","text":"phylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_outgroup.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to add an outgroup to any phylogeny, in phylo or newick format — tree_add_outgroup","title":"Function to add an outgroup to any phylogeny, in phylo or newick format — tree_add_outgroup","text":"Function add outgroup phylogeny, phylo newick format","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_outgroup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to add an outgroup to any phylogeny, in phylo or newick format — tree_add_outgroup","text":"","code":"tree_add_outgroup(tree = NULL, outgroup = \"outgroup\")"},{"path":"http://phylotastic.org/datelife/reference/tree_add_outgroup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to add an outgroup to any phylogeny, in phylo or newick format — tree_add_outgroup","text":"tree tree either newick character string phylo object. outgroup character vector name outgroup. length>1, first element used.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_add_outgroup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to add an outgroup to any phylogeny, in phylo or newick format — tree_add_outgroup","text":"phylo object root edge.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a tree is a phylo class object otherwise it uses input_process.\nAdditionally it can check if tree is a chronogram with phylo_check — tree_check","title":"Checks if a tree is a phylo class object otherwise it uses input_process.\nAdditionally it can check if tree is a chronogram with phylo_check — tree_check","text":"Checks tree phylo class object otherwise uses input_process. Additionally can check tree chronogram phylo_check","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a tree is a phylo class object otherwise it uses input_process.\nAdditionally it can check if tree is a chronogram with phylo_check — tree_check","text":"","code":"tree_check(tree = NULL, ...)"},{"path":"http://phylotastic.org/datelife/reference/tree_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a tree is a phylo class object otherwise it uses input_process.\nAdditionally it can check if tree is a chronogram with phylo_check — tree_check","text":"tree tree either newick character string phylo object. ... Arguments passed phylo_check brlen Boolean. TRUE checks phylo object branch lengths. dated Boolean. TRUE checks phylo object ultrametric.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a tree is a phylo class object otherwise it uses input_process.\nAdditionally it can check if tree is a chronogram with phylo_check — tree_check","text":"tree correctly formatted, returns phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_fix_brlen.html","id":null,"dir":"Reference","previous_headings":"","what":"Take a tree with branch lengths and fix negative or zero length branches. — tree_fix_brlen","title":"Take a tree with branch lengths and fix negative or zero length branches. — tree_fix_brlen","text":"Take tree branch lengths fix negative zero length branches.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_fix_brlen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Take a tree with branch lengths and fix negative or zero length branches. — tree_fix_brlen","text":"","code":"tree_fix_brlen( tree = NULL, fixing_criterion = \"negative\", fixing_method = 0, ultrametric = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/tree_fix_brlen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Take a tree with branch lengths and fix negative or zero length branches. — tree_fix_brlen","text":"tree tree either newick character string phylo object. fixing_criterion character vector specifying type branch length fixed: \"negative\" \"zero\" (number 0 also allowed). fixing_method character vector specifying method fix branch lengths: \"bladj\", \"mrbayes\" number assigned branches meeting fixing_criterion ultrametric Boolean indicating whether force ultrametric .","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_fix_brlen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Take a tree with branch lengths and fix negative or zero length branches. — tree_fix_brlen","text":"phylo object negative zero branch lengths.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_from_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","title":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","text":"uses taxize package's wrapper Global Names Resolver get taxonomic paths vector taxa pass . Sources vector source labels order (though works best everything uses taxonomy, recommend just one source). can see options taxize::gnr_datasources(). default Catalogue Life. output phylo object (typically many singleton nodes collapse_singles FALSE: nodes one descendant (like \"Homo\" \"Homo sapiens\" descendant) singletons typically node.labels","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_from_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","text":"","code":"tree_from_taxonomy( taxa, sources = \"Catalogue of Life\", collapse_singles = TRUE )"},{"path":"http://phylotastic.org/datelife/reference/tree_from_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","text":"taxa Vector taxon names sources Vector names preferred sources; see taxize::gnr_datasources(). Currently supports 100 taxonomic resources, see details. collapse_singles true, collapses singleton nodes","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_from_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","text":"list containing phylo object resolved names vector unresolved names","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_from_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gets a taxonomic tree from a vector of taxa — tree_from_taxonomy","text":"","code":"if (FALSE) # This is a flag for package development. You are welcome to run the example. taxa <- c( \"Homo sapiens\", \"Ursus arctos\", \"Pan paniscus\", \"Tyrannosaurus rex\", \"Ginkgo biloba\", \"Vulcan\", \"Klingon\" ) results <- tree_from_taxonomy(taxa) #> Error in lapply(x, f): object 'taxa' not found print(results$unresolved) # The taxa that do not match #> Error in print(results$unresolved): object 'results' not found ape::plot.phylo(results$phy) # may generate warnings due to problems with singletons #> Error in ape::plot.phylo(results$phy): object 'results' not found ape::plot.phylo(ape::collapse.singles(results$phy), show.node.label = TRUE) #> Error in ape::collapse.singles(results$phy): object 'results' not found # got rid of singles, but this also removes a lot of the node.labels # end dontrun"},{"path":"http://phylotastic.org/datelife/reference/tree_get_node_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. — tree_get_node_data","title":"Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. — tree_get_node_data","text":"Get node numbers, node names, descendant tip numbers labels nodes tree, node ages dated trees.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_get_node_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. — tree_get_node_data","text":"","code":"tree_get_node_data( tree = NULL, nodes = NULL, node_data = c(\"node_number\", \"node_label\", \"node_age\", \"descendant_tips_number\", \"descendant_tips_label\") )"},{"path":"http://phylotastic.org/datelife/reference/tree_get_node_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. — tree_get_node_data","text":"tree tree either newick character string phylo object. nodes Numeric vector node numbers want obtain data. Default NULL: obtain data nodes tree. node_data character vector containing one : \"node_number\", \"node_label\", \"node_age\", \"descendant_tips_number\", \"descendant_tips_label\"","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_get_node_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. — tree_get_node_data","text":"list","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_get_singleton_outgroup.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify the presence of a single lineage outgroup in a phylogeny — tree_get_singleton_outgroup","title":"Identify the presence of a single lineage outgroup in a phylogeny — tree_get_singleton_outgroup","text":"Identify presence single lineage outgroup phylogeny","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_get_singleton_outgroup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify the presence of a single lineage outgroup in a phylogeny — tree_get_singleton_outgroup","text":"","code":"tree_get_singleton_outgroup(tree = NULL)"},{"path":"http://phylotastic.org/datelife/reference/tree_get_singleton_outgroup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify the presence of a single lineage outgroup in a phylogeny — tree_get_singleton_outgroup","text":"tree tree either newick character string phylo object.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_get_singleton_outgroup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify the presence of a single lineage outgroup in a phylogeny — tree_get_singleton_outgroup","text":"character vector name single lineage outgroup. Returns NA none.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_node_tips.html","id":null,"dir":"Reference","previous_headings":"","what":"To get tip numbers descending from any given node of a tree — tree_node_tips","title":"To get tip numbers descending from any given node of a tree — tree_node_tips","text":"get tip numbers descending given node tree","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_node_tips.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"To get tip numbers descending from any given node of a tree — tree_node_tips","text":"","code":"tree_node_tips(tree = NULL, node = NULL, curr = NULL)"},{"path":"http://phylotastic.org/datelife/reference/tree_node_tips.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"To get tip numbers descending from any given node of a tree — tree_node_tips","text":"tree phylogenetic tree object class \"phylo\". node integer specifying node number tree. curr set previously stored node numbers - used recursive function calls.","code":""},{"path":"http://phylotastic.org/datelife/reference/tree_node_tips.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"To get tip numbers descending from any given node of a tree — tree_node_tips","text":"numeric vector tip numbers descending node","code":""},{"path":"http://phylotastic.org/datelife/reference/treebase_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","title":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","text":"Information contributors, authors, study ids clades studies chronograms Open tree Life","code":""},{"path":"http://phylotastic.org/datelife/reference/treebase_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","text":"","code":"treebase_cache"},{"path":"http://phylotastic.org/datelife/reference/treebase_cache.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","text":"list five data sets tb.author.pretty dataframe two elements: author names number studies TreeBase authored tb.author.results dataframe two elements: author names study identifiers","code":""},{"path":"http://phylotastic.org/datelife/reference/treebase_cache.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","text":"TreeBASE database, longer available online https://en.wikipedia.org/wiki/TreeBASE","code":""},{"path":"http://phylotastic.org/datelife/reference/treebase_cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life — treebase_cache","text":"Generated make_treebase_cache()","code":""},{"path":"http://phylotastic.org/datelife/reference/update_all_cached.html","id":null,"dir":"Reference","previous_headings":"","what":"Update all data files as data objects for the package — update_all_cached","title":"Update all data files as data objects for the package — update_all_cached","text":"includes opentree chronograms, contributors, treebase curators speed, datelife caches chronograms information. Running (within checked version datelife) refresh . git commit git push back","code":""},{"path":"http://phylotastic.org/datelife/reference/update_all_cached.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update all data files as data objects for the package — update_all_cached","text":"","code":"update_all_cached()"},{"path":"http://phylotastic.org/datelife/reference/update_all_cached.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update all data files as data objects for the package — update_all_cached","text":"None","code":""},{"path":"http://phylotastic.org/datelife/reference/update_datelife_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an updated OpenTree chronograms database object — update_datelife_cache","title":"Create an updated OpenTree chronograms database object — update_datelife_cache","text":"function calls get_opentree_chronograms() update OpenTree chronograms database cached datelife. option write updated object .Rdata file, independent opentree_chronograms data object can load data(\"opentree_chronograms\", package = \"datelife\").","code":""},{"path":"http://phylotastic.org/datelife/reference/update_datelife_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an updated OpenTree chronograms database object — update_datelife_cache","text":"","code":"update_datelife_cache( write = TRUE, updated_name = \"opentree_chronograms_updated\", file_path = file.path(tempdir()), ... )"},{"path":"http://phylotastic.org/datelife/reference/update_datelife_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an updated OpenTree chronograms database object — update_datelife_cache","text":"write Defaults TRUE, saves .Rdata file named indicated argument name, containing available chronograms Open Tree Life. Saves path indicated argument path. updated_name Used write = TRUE. Defaults \"opentree_chronograms_updated\". character vector length one indicating name assign updated OpenTree chronogram database object \".Rdata\" file. example, name = \"my_database\", function assign updated chronogram database object named my_database write file named \"my_database.Rdata\" path indicated argument file_path. file_path Used write = TRUE. character vector length 1 indicating path write updated database \".Rdata\" file , excluding file name. Defaults temporary directory obtained base::tempdir() formatted base::file.path(). ... Arguments passed get_opentree_chronograms max_tree_count Default \"\", gets available chronograms. testing purposes, numeric value indicating max number trees cached.","code":""},{"path":"http://phylotastic.org/datelife/reference/update_datelife_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an updated OpenTree chronograms database object — update_datelife_cache","text":"list 4 elements: authors list lists author names original studies published chronograms currently stored Open Tree Life database. curators list lists curator names uploaded chronograms Open Tree Life database. studies list study identifiers original studies published chronograms currently stored Open Tree Life database. trees multiPhylo object storing chronograms Open Tree Life database. update character vector indicating time database object last updated. version character vector indicating datelife package version object last updated.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"use_all_calibrations generates one multiple chronograms (.e., phylogenetic trees branch lengths proportional time) dating tree topology given phy, secondary calibrations given calibrations, using algorithm specified argument dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"","code":"use_all_calibrations( phy = NULL, calibrations = NULL, each = FALSE, dating_method = \"bladj\", ... )"},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"phy phylo object use tree topology. calibrations calibrations object, output get_all_calibrations(). Boolean, default FALSE: calibrations returned data.frame. TRUE, calibrations chronogram returned separate data frames. dating_method Tree dating algorithm use. Options \"bladj\" \"pathd8\" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ). ... Arguments passed use_calibrations type type age use calibration. Options \"median\", \"mean\", \"min\", \"max\".","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"phylo multiPhylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"phy branch lengths, dating_method ignores, function applies secondary calibrations date tree BLADJ algorithm. See make_bladj_tree() use_calibrations_bladj(). phy branch lengths, function can use PATHd8 algorithm. See use_calibrations_pathd8().","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"more","dir":"Reference","previous_headings":"","what":"More","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"output object stores used calibrations dating_method attributes(output)$datelife_calibrations attributes(output)$dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_all_calibrations.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations","text":"Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). \"Phylocom: software analysis phylogenetic community structure trait evolution\". Bioinformatics, 24(18), doi:10.1093/bioinformatics/btn358 . Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007). \"Estimating divergence times large phylogenetic trees\". Systematic biology, 56(5), 741-752. doi:10.1080/10635150701613783 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Date a given tree topology using a combined set of given calibrations — use_calibrations","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"use_calibrations combines given calibrations uses constraints perform dating analysis given tree topology, using BLADJ branch lengths, PATHd8 given tree topology initial branch lengths.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"","code":"use_calibrations( phy = NULL, calibrations = NULL, dating_method = \"bladj\", type = \"median\", ... )"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"phy phylo object use tree topology. calibrations calibrations object, output get_all_calibrations(). dating_method Tree dating algorithm use. Options \"bladj\" \"pathd8\" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ). type type age use calibration. Options \"median\", \"mean\", \"min\", \"max\". ... Arguments passed use_calibrations_pathd8 expand much expand step get consistent calibrations. 0 1. giveup many expansions try giving ","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"phylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"phy branch lengths, dating_method ignores, function applies secondary calibrations date tree BLADJ algorithm. See make_bladj_tree() use_calibrations_bladj(). phy branch lengths, function can use PATHd8 algorithm. See use_calibrations_pathd8().","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations.html","id":"more","dir":"Reference","previous_headings":"","what":"More","title":"Date a given tree topology using a combined set of given calibrations — use_calibrations","text":"output object stores used calibrations dating_method attributes(output)$datelife_calibrations attributes(output)$dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":null,"dir":"Reference","previous_headings":"","what":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"function use_calibrations_bladj prepares input BLADJ calls make_bladj_tree().","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"","code":"use_calibrations_bladj(phy = NULL, calibrations, type = \"median\", root_age)"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"phy phylo object without branch lengths. calibrations data.frame secondary calibrations pair taxon names phy, usually obtained get_all_calibrations(). type type age use calibration. Options \"median\", \"mean\", \"min\", \"max\". root_age Numeric specifying age root. used ages root node calibrations argument. missing, NULL, numeric, value oldest calibration plus one unit mean differences across calibrations, used root calibration. one single age point provided calibrations, root age set 10% age single calibration.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"chronogram: phylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"BLADJ algorithm part Phylocom software, presented Webb et al. (2008) doi:10.1093/bioinformatics/btn358 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj","text":"Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). \"Phylocom: software analysis phylogenetic community structure trait evolution\". Bioinformatics, 24(18), doi:10.1093/bioinformatics/btn358 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":null,"dir":"Reference","previous_headings":"","what":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"function prepares input BLADJ calls make_bladj_tree()","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"","code":"use_calibrations_bladj.matchedCalibrations( calibrations, type = \"mean\", root_age = NULL )"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"calibrations data.frame secondary calibrations pair taxon names phy, usually obtained get_all_calibrations(). type type age use calibration. Options \"median\", \"mean\", \"min\", \"max\". root_age Numeric specifying age root, provided user. used time calibrations root node chronograms database. NULL numeric, maximum calibration age plus one unit sd (calculated stats::sd()) node ages available tree used root calibration. one calibration available whole tree, root node age proportional 1.1 age calibration.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"phylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"BLADJ algorithm part Phylocom software, presented Webb et al. (2008) doi:10.1093/bioinformatics/btn358 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_bladj.matchedCalibrations.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations","text":"Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). \"Phylocom: software analysis phylogenetic community structure trait evolution\". Bioinformatics, 24(18), doi:10.1093/bioinformatics/btn358 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":null,"dir":"Reference","previous_headings":"","what":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"use_calibrations_each wraps use_calibrations take set given calibrations use independently constraints BLADJ PATHd8 date given tree topology.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"","code":"use_calibrations_each(phy = NULL, calibrations = NULL, ...)"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"phy phylo object use tree topology. calibrations calibrations object, output get_all_calibrations(). ... Arguments passed use_calibrations dating_method Tree dating algorithm use. Options \"bladj\" \"pathd8\" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ). type type age use calibration. Options \"median\", \"mean\", \"min\", \"max\".","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"multiPhylo object trees branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"phy branch lengths, dating_method ignores, function applies secondary calibrations date tree BLADJ algorithm. See make_bladj_tree() use_calibrations_bladj(). phy branch lengths, function can use PATHd8 algorithm. See use_calibrations_pathd8().","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_each.html","id":"more","dir":"Reference","previous_headings":"","what":"More","title":"Date a given tree topology by using a given list of calibrations independently,\nto generate multiple hypothesis of time of divergence — use_calibrations_each","text":"output object stores used calibrations dating_method attributes(output)$datelife_calibrations attributes(output)$dating_method.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":null,"dir":"Reference","previous_headings":"","what":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"use_calibrations_pathd8 uses secondary calibrations date tree initial branch lengths using PATHd8.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"","code":"use_calibrations_pathd8( phy = NULL, calibrations = NULL, expand = 0.1, giveup = 100 )"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"phy phylo object branch lengths. calibrations data.frame secondary calibrations pair taxon names phy, usually obtained get_all_calibrations(). expand much expand step get consistent calibrations. 0 1. giveup many expansions try giving ","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"phylo object branch lengths proportional time.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"function implements PATHd8 algorithm described Britton et al. (2007) doi:10.1080/10635150701613783 , geiger::PATHd8.phylo(). function first attempts use given calibrations fixed ages. fails (often due conflict calibrations), expand range minimum age maximum age try . repeat. expand = 0, uses summarized calibrations. cases, returns edge lengths relative time (maximum tree depth = 1) instead absolute time, given calibrations. case, function returns NA. issue PATHd8.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_pathd8.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8","text":"Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007). \"Estimating divergence times large phylogenetic trees\". Systematic biology, 56(5), 741-752. doi:10.1080/10635150701613783 .","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":null,"dir":"Reference","previous_headings":"","what":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"Date tree initial branch lengths treePL.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"","code":"use_calibrations_treePL(phy, calibrations)"},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"phy phylo object without branch lengths. calibrations data.frame secondary calibrations pair taxon names phy, usually obtained get_all_calibrations().","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"phylo object","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"function uses treePL described Smith, S. ., & O’Meara, B. C. (2012). doi:10.1093/bioinformatics/bts492 , function treePL.phylo. attempts use calibrations fixed ages. fails (often due conflict calibrations), expand range minimum age maximum age try . repeat. expand = 0, uses summarized calibrations. cases, returns edge lengths relative time (maximum tree depth = 1) instead absolute time, given calibrations. case, function returns NA. issue PATHd8.","code":""},{"path":"http://phylotastic.org/datelife/reference/use_calibrations_treePL.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Date a tree with initial branch lengths with treePL. — use_calibrations_treePL","text":"Smith, S. ., & O’Meara, B. C. (2012). \"treePL: divergence time estimation using penalized likelihood large phylogenies\". Bioinformatics, 28(20), 2689-2690, doi:10.1093/bioinformatics/bts492 .","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v069","dir":"Changelog","previous_headings":"","what":"datelife v0.6.9","title":"datelife v0.6.9","text":"fix bug check_ott_input() fix bug make_datelife_query() getting ott ids use spaces instead “_” run tnrs, avoids bug rotl::tnrs_match_names() v3.0.14 faster accurate way get study ids tree ids opentree API get_opentree_chronograms() branch lengths Myrs, relative time. update chronogram database, now 292 chronograms.","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v068","dir":"Changelog","previous_headings":"","what":"datelife v0.6.8","title":"datelife v0.6.8","text":"CRAN release: 2023-06-19 fix bug function extract_calibrations_phylo() update messages calibrations_match() add faster function retrieve descendants updates new rotl version fix uri DESCRIPTION","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v067","dir":"Changelog","previous_headings":"","what":"datelife v0.6.7","title":"datelife v0.6.7","text":"CRAN release: 2023-05-09 added vignette bold data workflow can use root age provided user root age, provides heavy warning uses age maximum calibration available plus one unit standard deviation – multiple calibrations available, plus 0.1*calibration age one calibration available. update links pkgdown/badges.Rmd pkgdown/presentation.Rmd","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v066","dir":"Changelog","previous_headings":"","what":"datelife v0.6.6","title":"datelife v0.6.6","text":"CRAN release: 2022-12-15 congruify_and_mrca_phylo() extract_calibrations_phylo() congruify_and_check() filters results congruify_and_mrca_phylo() inherit data.frame; usually happens congruification fails correctly assigns congruified phy attribute use_calibrations_bladj.matchedCalibrations() correctly uses calibrations argument get_ott_children() error handling OpenTree APIs might , internet connection various fixes make_datelife_query() et al. functions added new vignette making datelife query functions (allows testing various functionalities)","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v065","dir":"Changelog","previous_headings":"","what":"datelife v0.6.5","title":"datelife v0.6.5","text":"CRAN release: 2022-06-21 updated opentree_chronograms object. now 253 chronograms Open Tree Life uses “xz” compression. set test examples added functions matrix_to_table matrices_to_table go matrix patristic distances table taxon name pairs respective node ages. bug fix use_calibrations_bladj used element $present_calibrations instead $matched_calibrations get_otol_chronogram another name call get_opentree_chronograms added taxonomic source options argument make_datelife_query. can choose OTT, NCBI, IRMNG GBIF. function congruify_and_mrca: output congruified topology nodelables attribute. use_calibrations_bladj takes output congruify_and_mrca functions. added function method congruify_and_mrca","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v061","dir":"Changelog","previous_headings":"","what":"datelife v0.6.1","title":"datelife v0.6.1","text":"CRAN release: 2022-01-31 get_otol_chronograms updated renamed get_opentree_chronograms Update match_all_calibrations Added summary method datelifeResult objects Added “” section describing return value attributes (rename “Attributes”) Eliminated unnecessary examples Vignettes: added case study vignette Description: added BiocManager package imports","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v060","dir":"Changelog","previous_headings":"","what":"datelife v0.6.0","title":"datelife v0.6.0","text":"CRAN release: 2022-01-17 Dependencies: Bioconductor packages used conditionally Package website pkgdown documentation: expanded functions examples function files written tempdir() function rename: get_biggest_phylo get_biggest_multiphylo","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v050","dir":"Changelog","previous_headings":"","what":"datelife v0.5.0","title":"datelife v0.5.0","text":"datelife_query_check deprecated use_each_calibration renamed use_calibrations_each plotting functions moved datelifeplot package","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v031","dir":"Changelog","previous_headings":"","what":"datelife v0.3.1","title":"datelife v0.3.1","text":"Now muscle mafft can used alignment BOLD sequences","code":""},{"path":"http://phylotastic.org/datelife/news/index.html","id":"datelife-v0219","dir":"Changelog","previous_headings":"","what":"datelife v0.2.19","title":"datelife v0.2.19","text":"MrBayes TreePL dating methods Fully ultrametric summary chronograms datelife() outputs Overlay lineage time plots source chronograms Groves summarize trees","code":""}]
+[{"path":"http://phylotastic.org/datelife/README.knit.html","id":null,"dir":"","previous_headings":"","what":"Welcome to DateLife’s R package GitHub repository!","title":"Welcome to DateLife’s R package GitHub repository!","text":"Get phylogenetic tree branch lengths proportional geologic time (aka chronogram) two lineages interest . Use datelife R package locally, DateLife’s website search chronograms available lineages Open Tree Life’s tree store. can also date phylogenetic tree making (choosing one literature), using node ages chronograms found datelife, using congruification method (Eastman et al. 2013) implemented geiger (Harmon et al. 2008). datelife developed part phylotastic (NSF-funded) project, still development. Installation Citation Feedback info developers License","code":""},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"installation","dir":"","previous_headings":"","what":"1. Installation","title":"Welcome to DateLife’s R package GitHub repository!","text":"accepted CRAN, datelifes stable version available installation : now, can install development version GitHub repository:","code":"install.packages(\"datelife\") devtools::install_github(\"phylotastic/datelife\")"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"citation","dir":"","previous_headings":"","what":"2. Citation","title":"Welcome to DateLife’s R package GitHub repository!","text":"use datelife publication, please cite R package accompanying paper: O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright , Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2022). datelife: Go List Taxa Tree Chronogram using Open Scientific Data Time Lineage Divergence. R package version 0.5.0. Sanchez-Reyes L, O’Meara B (2019). “datelife: Leveraging databases analytical tools reveal dated Tree Life.” bioRxiv, 782094. doi: 10.1101/782094. can get citations bibtex entry : .bibtex files available","code":"citation(\"datelife\") toBibtex(citation(\"datelife\"))"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"feedback-and-information-for-developers","dir":"","previous_headings":"","what":"3. Feedback and Information for Developers","title":"Welcome to DateLife’s R package GitHub repository!","text":"welcome encourage post GitHub issue comments, ideas questions datelife’s software website. want contribute code directly, welcome encourage pull requests.","code":""},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"function-documentation","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Function documentation:","title":"Welcome to DateLife’s R package GitHub repository!","text":"Package function documentation generated roxygen2:","code":"roxygen2::roxygenise()"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"styling-code","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Styling code:","title":"Welcome to DateLife’s R package GitHub repository!","text":"used package lintr check coding style:","code":"lintr::lint_package()"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"calculating-test-coverage","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Calculating test coverage:","title":"Welcome to DateLife’s R package GitHub repository!","text":"Code coverage calculated package covr: can see interactive report testing coverage: , find code zero coverage:","code":"cov <- covr::package_coverage() usethis::use_data(cov, overwrite = TRUE) covr::report(cov) covr::zero_coverage(cov)"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"releasing-to-cran","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Releasing to CRAN:","title":"Welcome to DateLife’s R package GitHub repository!","text":"able release CRAN, first step pass check. run local check, can use command R CMD check terminal. , change directories one working clone datelife repo: Generate tar ball package running R CMD build package-name: Finally, run R CMD check package-tar-ball tar ball just generated: access different OS test package , rhub package allows remote testing variety OS command:","code":"cd ../ R CMD build datelife R CMD check datelife_0.6.0.tar.gz rhub::check_for_cran()"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"generating-datelifes-hexsticker","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Generating datelife’s hexsticker:","title":"Welcome to DateLife’s R package GitHub repository!","text":"Code used generate current datelife’s logo hexsticker data-raw/hexsticker-current.R","code":""},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"rendering-the-vignettes","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Rendering the vignettes:","title":"Welcome to DateLife’s R package GitHub repository!","text":"","code":"knitr::knit(\"vignettes/Getting_started_with_datelife.Rmd\")"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"creating-a-website-for-the-package","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Creating a website for the package","title":"Welcome to DateLife’s R package GitHub repository!","text":"Using pkgdown quite straightforwrd fun:","code":"usethis::use_pkgdown() pkgdown::build_site()"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"submitting-to-cran","dir":"","previous_headings":"3. Feedback and Information for Developers","what":"Submitting to CRAN","title":"Welcome to DateLife’s R package GitHub repository!","text":"","code":"devtools::release()"},{"path":"http://phylotastic.org/datelife/README.knit.html","id":"license","dir":"","previous_headings":"","what":"4. License","title":"Welcome to DateLife’s R package GitHub repository!","text":"package free open source software, licensed GPL.","code":""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"what-can-you-get-with-datelife","dir":"Articles","previous_headings":"","what":"What can you get with datelife?","title":"Getting started","text":"datelife user, can get age data organisms interest several forms: MRCA: Get age recent common ancestor (MRCA) organisms. Original chronogram: Get chronograms original publications, pruned contain organisms . Biggest chronogram: Get original chronogram organisms interest present tips. Summary chronogram: Obtain single chronogram, summarized using data original chronograms. summary chronogram can calculated using different methods. can also apply obtained age data date phylogenetic tree topology organisms interest.","code":""},{"path":[]},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"processing-your-organism-names","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"1. Processing your organism names","title":"Getting started","text":"function make_datelife_query processes taxon names organisms interest structures datelifeQuery object. datelifeQuery object list three elements: $cleaned_names: character vector “cleaned” taxon names, $ott_ids: numeric vector OpenTree Taxonomic identifiers (OTT ids), $phy: input tree phylo object NA none provided. allows us straightforwardly use processed taxon names later perform search ages across datelife chronogram database well downstream analyses. two alternative ways processing organism names datelife:","code":""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"a-from-a-set-of-organism-taxonomic-names","dir":"Articles","previous_headings":"How do you use datelife to get these data? > 1. Processing your organism names","what":"a) From a set of organism taxonomic names","title":"Getting started","text":"can provide taxon names character vector single comma separated string names. example, running following: Gives result running: Note can use underscores spaces separate binomial scientific names datelife process .","code":"datelife::make_datelife_query(input = c(\"Delphinus_delphis\", \"Gallus gallus\", \"elephas Maximus\", \"felis_catus\", \"homo-sapiens\")) #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is not a phylogeny. #> DateLife query done! #> $cleaned_names #> [1] \"Delphinus delphis\" \"Gallus gallus\" \"elephas Maximus\" #> [4] \"felis catus\" #> #> $ott_ids #> NULL #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\" datelife::make_datelife_query(input = \"Delphinus_delphis, Gallus gallus, elephas Maximus, felis_catus, homo-sapiens\") #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is not a phylogeny. #> DateLife query done! #> $cleaned_names #> [1] \"Delphinus delphis\" \"Gallus gallus\" \"elephas Maximus\" #> [4] \"felis catus\" #> #> $ott_ids #> NULL #> #> $phy #> [1] NA #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"b-from-a-tree-with-organism-taxonomic-names-as-tip-labels","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"b) From a tree with organism taxonomic names as tip labels","title":"Getting started","text":"can also provide taxon names organisms interest labels tips phylogenetic tree. can provide tree newick string: can also provide tree phylo object. already tree phylo object, can use directly. example, first convert newick string phylo. can function read.tree ape package: Now save datelifeQuery object next section:","code":"newick <- \"((Elephas_maximus,(Homo_sapiens,(Delphinus_delphis, Felis_silvestris))), Gallus_gallus);\" datelife::make_datelife_query(input = newick) #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is a phylogeny and it is correcly formatted. #> DateLife query done! #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \" Felis silvestris\" #> [4] \" Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, _Felis_silvestris, _Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\" phylo <- ape::read.tree(text = newick) datelife::make_datelife_query(input = phylo) #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is a phylogeny and it is correcly formatted. #> DateLife query done! #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\" my_datelife_query <- datelife::make_datelife_query(input = phylo) #> ... Making a DateLife query. #> ... Phylo-processing 'input'. #> 'input' is a phylogeny and it is correctly formatted. #> DateLife query done!"},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"searching-the-chronogram-database","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"2. Searching the chronogram database","title":"Getting started","text":"datelife_search function takes datelifeQuery object goes datelife chronogram database find chronograms matching least two taxon names:","code":"datelife::datelife_search(input = my_datelife_query) #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> 4 phylogenetic trees"},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"summarizing-chronogram-search-results","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"3. Summarizing chronogram search results","title":"Getting started","text":"datelife_search also summarize results chronogram database search . default, give original chronograms matching search, phylo multiPhylo object. can specify format desire summary results argument summary_format. different summary formats choose :","code":""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"citations","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"Citations","title":"Getting started","text":"summary_format = \"citations\" gives back study citations original chronograms matching search:","code":"citations <- datelife::datelife_search(input = my_datelife_query, summary_format = \"citations\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> [1] \"Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512\" #> [2] \"Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512\" #> [3] \"Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512\" #> [4] \"Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845\" #> attr(,\"datelife_result\") #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Delphinus delphis #> Elephas maximus 0.0 202.6 #> Delphinus delphis 202.6 0.0 #> Felis silvestris 202.6 177.0 #> Felis silvestris #> Elephas maximus 202.6 #> Delphinus delphis 177.0 #> Felis silvestris 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Felis silvestris #> Elephas maximus 0.0 192.2 #> Felis silvestris 192.2 0.0 #> Delphinus delphis 192.2 173.6 #> Delphinus delphis #> Elephas maximus 192.2 #> Felis silvestris 173.6 #> Delphinus delphis 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Delphinus delphis Felis silvestris #> Delphinus delphis 0.0 179.6 #> Felis silvestris 179.6 0.0 #> Elephas maximus 221.6 221.6 #> Elephas maximus #> Delphinus delphis 221.6 #> Felis silvestris 221.6 #> Elephas maximus 0.0 #> #> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845` #> Felis silvestris Delphinus delphis #> Felis silvestris 0.0000 156.7850 #> Delphinus delphis 156.7850 0.0000 #> Elephas maximus 210.0193 210.0193 #> Gallus gallus 641.0476 641.0476 #> Elephas maximus Gallus gallus #> Felis silvestris 210.0193 641.0476 #> Delphinus delphis 210.0193 641.0476 #> Elephas maximus 0.0000 641.0476 #> Gallus gallus 641.0476 0.0000 #> #> attr(,\"class\") #> [1] \"datelifeResult\" #> attr(,\"datelife_query\") #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"mrca-ages","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"MRCA ages","title":"Getting started","text":"summary_format = \"mrca\" gives back age MRCA organisms interest:","code":"mrca <- datelife::datelife_search(input = my_datelife_query, summary_format = \"mrca\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 101.3000 #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 96.1000 #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 110.8000 #> Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> 320.5238 #> attr(,\"datelife_result\") #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Delphinus delphis #> Elephas maximus 0.0 202.6 #> Delphinus delphis 202.6 0.0 #> Felis silvestris 202.6 177.0 #> Felis silvestris #> Elephas maximus 202.6 #> Delphinus delphis 177.0 #> Felis silvestris 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Felis silvestris #> Elephas maximus 0.0 192.2 #> Felis silvestris 192.2 0.0 #> Delphinus delphis 192.2 173.6 #> Delphinus delphis #> Elephas maximus 192.2 #> Felis silvestris 173.6 #> Delphinus delphis 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Delphinus delphis Felis silvestris #> Delphinus delphis 0.0 179.6 #> Felis silvestris 179.6 0.0 #> Elephas maximus 221.6 221.6 #> Elephas maximus #> Delphinus delphis 221.6 #> Felis silvestris 221.6 #> Elephas maximus 0.0 #> #> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845` #> Felis silvestris Delphinus delphis #> Felis silvestris 0.0000 156.7850 #> Delphinus delphis 156.7850 0.0000 #> Elephas maximus 210.0193 210.0193 #> Gallus gallus 641.0476 641.0476 #> Elephas maximus Gallus gallus #> Felis silvestris 210.0193 641.0476 #> Delphinus delphis 210.0193 641.0476 #> Elephas maximus 0.0000 641.0476 #> Gallus gallus 641.0476 0.0000 #> #> attr(,\"class\") #> [1] \"datelifeResult\" #> attr(,\"datelife_query\") #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"newick-strings","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"Newick strings","title":"Getting started","text":"summary_format = \"newick_all\" summary_format = \"newick_sdm\" summary_format = \"newick_median\"","code":"newick_all <- datelife::datelife_search(input = my_datelife_query, summary_format = \"newick_all\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> \"((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3);\" #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> \"((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1);\" #> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> \"((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8);\" #> Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> \"((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);\" #> attr(,\"datelife_result\") #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Delphinus delphis #> Elephas maximus 0.0 202.6 #> Delphinus delphis 202.6 0.0 #> Felis silvestris 202.6 177.0 #> Felis silvestris #> Elephas maximus 202.6 #> Delphinus delphis 177.0 #> Felis silvestris 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Felis silvestris #> Elephas maximus 0.0 192.2 #> Felis silvestris 192.2 0.0 #> Delphinus delphis 192.2 173.6 #> Delphinus delphis #> Elephas maximus 192.2 #> Felis silvestris 173.6 #> Delphinus delphis 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Delphinus delphis Felis silvestris #> Delphinus delphis 0.0 179.6 #> Felis silvestris 179.6 0.0 #> Elephas maximus 221.6 221.6 #> Elephas maximus #> Delphinus delphis 221.6 #> Felis silvestris 221.6 #> Elephas maximus 0.0 #> #> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845` #> Felis silvestris Delphinus delphis #> Felis silvestris 0.0000 156.7850 #> Delphinus delphis 156.7850 0.0000 #> Elephas maximus 210.0193 210.0193 #> Gallus gallus 641.0476 641.0476 #> Elephas maximus Gallus gallus #> Felis silvestris 210.0193 641.0476 #> Delphinus delphis 210.0193 641.0476 #> Elephas maximus 0.0000 641.0476 #> Gallus gallus 641.0476 0.0000 #> #> attr(,\"class\") #> [1] \"datelifeResult\" #> attr(,\"datelife_query\") #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\" newick_sdm <- datelife::datelife_search(input = my_datelife_query, summary_format = \"newick_sdm\") newick_median <- datelife::datelife_search(input = my_datelife_query, summary_format = \"newick_median\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Trying with overlap = 2 #> Registered S3 method overwritten by 'compare': #> method from #> print.comparison testthat #> Success! #> ... Calculating a median summary chronogram. #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> [1] \"((Elephas_maximus:103.154831,(Delphinus_delphis:87.650002,Felis_silvestris:87.650002)n3:15.504829)n2:217.369003,Gallus_gallus:320.523834)n1:1;\" #> attr(,\"datelife_result\") #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Delphinus delphis #> Elephas maximus 0.0 202.6 #> Delphinus delphis 202.6 0.0 #> Felis silvestris 202.6 177.0 #> Felis silvestris #> Elephas maximus 202.6 #> Delphinus delphis 177.0 #> Felis silvestris 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Elephas maximus Felis silvestris #> Elephas maximus 0.0 192.2 #> Felis silvestris 192.2 0.0 #> Delphinus delphis 192.2 173.6 #> Delphinus delphis #> Elephas maximus 192.2 #> Felis silvestris 173.6 #> Delphinus delphis 0.0 #> #> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512` #> Delphinus delphis Felis silvestris #> Delphinus delphis 0.0 179.6 #> Felis silvestris 179.6 0.0 #> Elephas maximus 221.6 221.6 #> Elephas maximus #> Delphinus delphis 221.6 #> Felis silvestris 221.6 #> Elephas maximus 0.0 #> #> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845` #> Felis silvestris Delphinus delphis #> Felis silvestris 0.0000 156.7850 #> Delphinus delphis 156.7850 0.0000 #> Elephas maximus 210.0193 210.0193 #> Gallus gallus 641.0476 641.0476 #> Elephas maximus Gallus gallus #> Felis silvestris 210.0193 641.0476 #> Delphinus delphis 210.0193 641.0476 #> Elephas maximus 0.0000 641.0476 #> Gallus gallus 641.0476 0.0000 #> #> attr(,\"class\") #> [1] \"datelifeResult\" #> attr(,\"datelife_query\") #> $cleaned_names #> [1] \"Elephas maximus\" \"Delphinus delphis\" \"Felis silvestris\" #> [4] \"Gallus gallus\" #> #> $ott_ids #> NULL #> #> $phy #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> #> Rooted; no branch lengths. #> #> attr(,\"class\") #> [1] \"datelifeQuery\""},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"phylo-objects","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"phylo objects","title":"Getting started","text":"summary_format = \"phylo_sdm\" summary_format = \"phylo_median\" summary_format = \"phylo_all\" summary_format = \"phylo_biggest\"","code":"phylo_sdm <- datelife::datelife_search(input = my_datelife_query, summary_format = \"phylo_sdm\") phylo_median <- datelife::datelife_search(input = my_datelife_query, summary_format = \"phylo_median\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Trying with overlap = 2 #> Success! #> ... Calculating a median summary chronogram. #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus #> Node labels: #> n1, n2, n3 #> #> Rooted; includes branch lengths. phylo_all <- datelife::datelife_search(input = my_datelife_query, summary_format = \"phylo_all\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> 4 phylogenetic trees phylo_biggest <- datelife::datelife_search(input = my_datelife_query, summary_format = \"phylo_biggest\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Source chronograms from: #> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512 #> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845 #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> #> Phylogenetic tree with 4 tips and 3 internal nodes. #> #> Tip labels: #> Gallus_gallus, Felis_silvestris, Delphinus_delphis, Elephas_maximus #> #> Rooted; includes branch lengths."},{"path":"http://phylotastic.org/datelife/articles/Getting_started_with_datelife.html","id":"summary-tables","dir":"Articles","previous_headings":"How do you use datelife to get these data?","what":"Summary tables","title":"Getting started","text":"summary_format = \"html\" returns summary table “html” format cns open read web browser. summary_format = \"data_frame\"","code":"html <- datelife::datelife_search(input = my_datelife_query, summary_format = \"html\") #> ... Running a DateLife search. #> ... Getting a DateLife result. #> DateLife result obtained! #> Input taxa presence across source chronograms: #> taxon chronograms #> 1 Elephas maximus 4/4 #> 2 Delphinus delphis 4/4 #> 3 Felis silvestris 4/4 #> 4 Gallus gallus 1/4 #> Input taxa completely absent from source chronograms: #> taxon #> 1 None #> DateLife search done! #> [1] \"
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