diff --git a/articles/simulation.html b/articles/simulation.html index d1bc864b..1864a128 100644 --- a/articles/simulation.html +++ b/articles/simulation.html @@ -342,9 +342,9 @@

Evaluating the settings#> Number of data generating functions: 8 #> Number of analyzing procedures: 6 #> Number of replications: 1 -#> Estimated replications per hour: 339 -#> Start of the simulation: 2024-01-12 08:50:52.573781 -#> End of the simulation: 2024-01-12 08:51:03.164747 +#> Estimated replications per hour: 322 +#> Start of the simulation: 2024-01-12 13:18:15.029658 +#> End of the simulation: 2024-01-12 13:18:26.198093

Analyzing the results diff --git a/pkgdown.yml b/pkgdown.yml index 494c8ad0..87b7739b 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,5 +5,5 @@ articles: demo: demo.html implement: implement.html simulation: simulation.html -last_built: 2024-01-12T08:48Z +last_built: 2024-01-12T13:16Z diff --git a/reference/as.list.lcMethod.html b/reference/as.list.lcMethod.html index 1269a757..8fd8583d 100644 --- a/reference/as.list.lcMethod.html +++ b/reference/as.list.lcMethod.html @@ -139,13 +139,13 @@

Examples

#> { #> mean(x, ..., na.rm = TRUE) #> } -#> <bytecode: 0x557f16e8f020> +#> <bytecode: 0x55fa8513d1a0> #> <environment: namespace:latrend> #> #> $standardize #> function (x, center = TRUE, scale = TRUE) #> UseMethod("scale") -#> <bytecode: 0x557f16edcd78> +#> <bytecode: 0x55fa851806e8> #> <environment: namespace:base> #> #> $method @@ -177,7 +177,7 @@

Examples

#> #> $formula #> Y ~ Time -#> <environment: 0x557f172c2588> +#> <environment: 0x55fa854c7768> #> as.list(method, args = c("id", "time")) @@ -188,7 +188,7 @@

Examples

#> [1] "Time" #> -if (require("kml")) { +if (require("kml")) { method <- lcMethodKML("Y", id = "Id", time = "Time") as.list(method) @@ -230,11 +230,11 @@

Examples

#> #> $distance #> function(){} -#> <environment: 0x557f1680f610> +#> <environment: 0x55fa812218f8> #> #> $centerMethod #> function(x){mean(x,na.rm=TRUE)} -#> <bytecode: 0x557f09f82958> +#> <bytecode: 0x55fa83bcafc0> #> <environment: namespace:longitudinalData> #> #> $startingCond diff --git a/reference/clusterProportions.html b/reference/clusterProportions.html index 23763fe6..d8689019 100644 --- a/reference/clusterProportions.html +++ b/reference/clusterProportions.html @@ -148,7 +148,7 @@

Examples

model <- latrend(method, latrendData, nClusters = 2) clusterProportions(model) #> A B -#> 0.4 0.6 +#> 0.6 0.4
diff --git a/reference/clusterSizes.html b/reference/clusterSizes.html index 16ec7271..5d18141a 100644 --- a/reference/clusterSizes.html +++ b/reference/clusterSizes.html @@ -139,7 +139,7 @@

Examples

model <- latrend(method, latrendData, nClusters = 2) clusterSizes(model) #> A B -#> 80 120 +#> 120 80 diff --git a/reference/formula.lcMethod.html b/reference/formula.lcMethod.html index 41746ca9..3a6e0cc9 100644 --- a/reference/formula.lcMethod.html +++ b/reference/formula.lcMethod.html @@ -116,7 +116,7 @@

Examples

method <- lcMethodLMKM(Y ~ Time, id = "Id", time = "Time")
 formula(method) # Y ~ Time
 #> Y ~ Time
-#> <environment: 0x557f25974f88>
+#> <environment: 0x55fa8febc100>
diff --git a/reference/formula.lcModel.html b/reference/formula.lcModel.html index 3bb628d8..f5454218 100644 --- a/reference/formula.lcModel.html +++ b/reference/formula.lcModel.html @@ -107,7 +107,7 @@

Examples

model <- latrend(method, data = latrendData) formula(model) # Y ~ Time #> Y ~ Time -#> <environment: 0x557f2262e360> +#> <environment: 0x55fa96a2de30> diff --git a/reference/index.html b/reference/index.html index f9bb0bdc..ef534d6a 100644 --- a/reference/index.html +++ b/reference/index.html @@ -283,7 +283,7 @@

All functions

Metrics

-

latrend-package _PACKAGE

+

latrend-package

latrend: A Framework for Clustering Longitudinal Data

@@ -595,11 +595,11 @@

All functions

Get the cluster membership of each trajectory

-

transformFitted transformFitted,NULL,lcModel-method transformFitted,matrix,lcModel-method transformFitted,list,lcModel-method transformFitted,data.frame,lcModel-method

+

transformFitted()

Helper function for custom lcModel classes implementing fitted.lcModel()

-

transformPredict transformPredict,NULL,lcModel-method transformPredict,vector,lcModel-method transformPredict,matrix,lcModel-method transformPredict,data.frame,lcModel-method

+

transformPredict()

Helper function for custom lcModel classes implementing predict.lcModel()

diff --git a/reference/interface-akmedoids.html b/reference/interface-akmedoids.html index bec58c74..b7d018a6 100644 --- a/reference/interface-akmedoids.html +++ b/reference/interface-akmedoids.html @@ -105,7 +105,7 @@

Arguments

See also

-

lcMethodAkmedoids akclustr

+

lcMethodAkmedoids akclustr

diff --git a/reference/latrend-generics.html b/reference/latrend-generics.html index bf55d32b..9d2fa740 100644 --- a/reference/latrend-generics.html +++ b/reference/latrend-generics.html @@ -148,10 +148,10 @@

Method- and model-specific generics defined by the latrend package

validate(method, data, envir, ...) -# S4 method for `NULL` +# S4 method for NULL getName(object, ...) -# S4 method for `NULL` +# S4 method for NULL getShortName(object, ...) diff --git a/reference/lcMethodAkmedoids.html b/reference/lcMethodAkmedoids.html index 12394f13..2784cba8 100644 --- a/reference/lcMethodAkmedoids.html +++ b/reference/lcMethodAkmedoids.html @@ -107,7 +107,7 @@

Arguments

...
-

Arguments passed to akmedoids::akclustr. +

Arguments passed to akmedoids::akclustr. The following external arguments are ignored: traj, id_field, k

@@ -144,12 +144,14 @@

See also

Examples

data(latrendData)
-if (require("akmedoids")) {
+if (require("akmedoids")) {
   method <- lcMethodAkmedoids(response = "Y", time = "Time", id = "Id", nClusters = 3)
   model <- latrend(method, data = latrendData)
 }
 #> Loading required package: akmedoids
-#> Error: 'akclustr' is not an exported object from 'namespace:akmedoids'
+#> [1] "Processing...."
+#> [1] ".............."
+#> [1] "solution of k = 3 determined!"
diff --git a/reference/lcMethodDtwclust.html b/reference/lcMethodDtwclust.html index 3cd3a67a..5195f761 100644 --- a/reference/lcMethodDtwclust.html +++ b/reference/lcMethodDtwclust.html @@ -160,13 +160,9 @@

Examples

#> #> Precomputing distance matrix... #> -#> Iteration 1: Changes / Distsum = 200 / 602.2515 -#> Iteration 2: Changes / Distsum = 5 / 424.9881 -#> Iteration 3: Changes / Distsum = 8 / 417.9849 -#> Iteration 4: Changes / Distsum = 10 / 414.0508 -#> Iteration 5: Changes / Distsum = 13 / 409.5495 -#> Iteration 6: Changes / Distsum = 10 / 407.0692 -#> Iteration 7: Changes / Distsum = 0 / 407.0692 +#> Iteration 1: Changes / Distsum = 200 / 543.5639 +#> Iteration 2: Changes / Distsum = 33 / 349.0671 +#> Iteration 3: Changes / Distsum = 0 / 349.0671 #> #> Elapsed time is 0.098 seconds. #> diff --git a/reference/lcMethodKML.html b/reference/lcMethodKML.html index 8e88266d..fcfeae47 100644 --- a/reference/lcMethodKML.html +++ b/reference/lcMethodKML.html @@ -137,7 +137,7 @@

See also

Examples

data(latrendData)
 
-if (require("kml")) {
+if (require("kml")) {
   method <- lcMethodKML("Y", id = "Id", time = "Time", nClusters = 3)
   model <- latrend(method, latrendData)
 }
diff --git a/reference/lcMethodMclustLLPA.html b/reference/lcMethodMclustLLPA.html
index b99b2650..307f1813 100644
--- a/reference/lcMethodMclustLLPA.html
+++ b/reference/lcMethodMclustLLPA.html
@@ -139,7 +139,7 @@ 
Examples

   model <- latrend(method, latrendData)
 }
 #> Loading required package: mclust
-#> Package 'mclust' version 6.0.0
+#> Package 'mclust' version 6.0.1
 #> Type 'citation("mclust")' for citing this R package in publications.
diff --git a/reference/lcMethodMixAK_GLMM.html b/reference/lcMethodMixAK_GLMM.html index 9cec1698..1d6a092c 100644 --- a/reference/lcMethodMixAK_GLMM.html +++ b/reference/lcMethodMixAK_GLMM.html @@ -169,14 +169,14 @@

Examples

#> random: ~Time #> #> Cluster sizes (K=3): -#> A B C -#> 79 (27.6%) 34 (42.1%) 87 (30.3%) +#> A B C +#> 84 (34.7%) 1 (20.1%) 115 (45.2%) #> #> Number of obs: 2000, strata (Id): 200 #> #> Scaled residuals: #> Min. 1st Qu. Median Mean 3rd Qu. Max. -#> -2.3943 -0.8828 0.1456 0.0000 0.9715 1.9116 +#> -2.7877 -0.7771 -0.2110 0.0000 0.9145 2.4144 #> diff --git a/reference/lcModel-1.png b/reference/lcModel-1.png index 8bf7c296..a0973bac 100644 Binary files a/reference/lcModel-1.png and b/reference/lcModel-1.png differ diff --git a/reference/min.lcModels.html b/reference/min.lcModels.html index b18557dc..f06f1086 100644 --- a/reference/min.lcModels.html +++ b/reference/min.lcModels.html @@ -150,14 +150,14 @@

Examples

#> formula: Y ~ Time #> #> Cluster sizes (K=3): -#> A B C -#> 72 (36%) 50 (25%) 78 (39%) +#> A B C +#> 120 (60%) 41 (20.5%) 39 (19.5%) #> #> Number of obs: 2000, strata (Id): 200 #> #> Scaled residuals: #> Min. 1st Qu. Median Mean 3rd Qu. Max. -#> -3.55483 -0.55670 -0.04454 0.00000 0.59256 5.41874 +#> -4.07173 -0.63323 0.03828 0.00000 0.66900 3.44575 #> diff --git a/reference/plot-lcModel-method-1.png b/reference/plot-lcModel-method-1.png index 83b32616..866c378d 100644 Binary files a/reference/plot-lcModel-method-1.png and b/reference/plot-lcModel-method-1.png differ diff --git a/reference/plotClusterTrajectories-1.png b/reference/plotClusterTrajectories-1.png index 59f70c88..98c0cfa6 100644 Binary files a/reference/plotClusterTrajectories-1.png and b/reference/plotClusterTrajectories-1.png differ diff --git a/reference/plotFittedTrajectories-1.png b/reference/plotFittedTrajectories-1.png index 615a2d5c..bbfa39a1 100644 Binary files a/reference/plotFittedTrajectories-1.png and b/reference/plotFittedTrajectories-1.png differ diff --git a/reference/predictAssignments.html b/reference/predictAssignments.html index 21dcc9a5..7fffd1af 100644 --- a/reference/predictAssignments.html +++ b/reference/predictAssignments.html @@ -147,7 +147,7 @@

See also

Examples

if (FALSE) {
 data(latrendData)
-if (require("kml")) {
+if (require("kml")) {
   model <- latrend(method = lcMethodKML("Y", id = "Id", time = "Time"), latrendData)
   predictAssignments(model, newdata = data.frame(Id = 999, Y = 0, Time = 0))
 }
diff --git a/reference/transformFitted.html b/reference/transformFitted.html
index 7ff26df5..ddcb61ba 100644
--- a/reference/transformFitted.html
+++ b/reference/transformFitted.html
@@ -102,7 +102,7 @@ 
Helper function for custom lcModel classes implementing fitted.lcModel()

     
transformFitted(pred, model, clusters)
 
-# S4 method for `NULL`,lcModel
+# S4 method for NULL,lcModel
 transformFitted(pred, model, clusters = NULL)
 
 # S4 method for matrix,lcModel
diff --git a/reference/transformPredict.html b/reference/transformPredict.html
index a4a6451b..2cb9b650 100644
--- a/reference/transformPredict.html
+++ b/reference/transformPredict.html
@@ -106,7 +106,7 @@ 
Helper function for custom lcModel classes implementing predict.lcModel()
     
transformPredict(pred, model, newdata)
 
-# S4 method for `NULL`,lcModel
+# S4 method for NULL,lcModel
 transformPredict(pred, model, newdata)
 
 # S4 method for vector,lcModel
diff --git a/reference/which.weight.html b/reference/which.weight.html
index adecc05c..2669b778 100644
--- a/reference/which.weight.html
+++ b/reference/which.weight.html
@@ -89,7 +89,7 @@ 
Value

     
Examples

     
x = c(.01, .69, .3)
 which.weight(x) #1, 2, or 3
-#> [1] 3
+#> [1] 2