Updated README and pkgdown home page with info on known issues relate…

…d to the first installation.

R/clinspacy.R

@@ -65,12 +65,12 @@ clinspacy_init <- function(miniconda = TRUE, use_linker = FALSE, linker_threshol
                                                                             threshold = linker_threshold, ...)
       }
       clinspacy_env$use_linker <- use_linker
-      message('Adding the UMLS entity linker to the spacy pipeline...')
+      message('Adding the UMLS entity linker to the spaCy pipeline...')
       clinspacy_env$nlp$add_pipe(clinspacy_env$linker)
       return(invisible())
     } else if (clinspacy_env$use_linker == TRUE & use_linker == FALSE) {
       clinspacy_env$use_linker <- use_linker
-      message('Removing the UMLS entity linker from the spacy pipeline...')
+      message('Removing the UMLS entity linker from the spaCy pipeline...')
       clinspacy_env$nlp$remove_pipe('EntityLinker')
       return(invisible())
     } else {

README.Rmd

@@ -40,13 +40,14 @@ library(clinspacy)
 
 ## Initiating clinspacy
 
+*Note: the very first time you run `clinspacy_init()` or `clinspacy()` after installing the package, you may receive an error stating that `spaCy` was unable to be imported because it was not found. Restarting your R session should resolve the issue.*
+
 Initiating clinspacy is optional. If you do not initiate the package using `clinspacy_init()`, it will be automatically initiated without the UMLS linker. The UMLS linker takes up ~12 GB of RAM, so if you would like to use the linker, you can initiate clinspacy with the linker. The linker can still be added on later by reinitiating with the `use_linker` argument set to `TRUE`.
 
 ```{r}
 clinspacy_init() # This is optional! The default functionality is to initiatie clinspacy without the UMLS linker
 ```
 
-
 ## Named entity recognition (without the UMLS linker)
 
 The `clinspacy()` function can take a single string, a character vector, or a data frame. It can output either a data frame or a file name.

README.md

@@ -28,6 +28,11 @@ library(clinspacy)
 
 ## Initiating clinspacy
 
+*Note: the very first time you run `clinspacy_init()` or `clinspacy()`
+after installing the package, you may receive an error stating that
+`spaCy` was unable to be imported because it was not found. Restarting
+your R session should resolve the issue.*
+
 Initiating clinspacy is optional. If you do not initiate the package
 using `clinspacy_init()`, it will be automatically initiated without the
 UMLS linker. The UMLS linker takes up \~12 GB of RAM, so if you would
@@ -434,8 +439,8 @@ clinspacy('This patient has diabetes and CKD stage 3 but no HTN.')
 #> 1            1 C0030705     patient     patient Patient or Disabled Group                        Patients     FALSE         FALSE
 #> 2            1 C1578481     patient     patient           Idea or Concept      Mail Claim Party - Patient     FALSE         FALSE
 #> 3            1 C1578484     patient     patient           Idea or Concept Relationship modifier - Patient     FALSE         FALSE
-#> 4            1 C1578486     patient     patient      Intellectual Product  Disabled Person Code - Patient     FALSE         FALSE
-#> 5            1 C1705908     patient     patient                  Organism              Veterinary Patient     FALSE         FALSE
+#> 4            1 C1578485     patient     patient      Intellectual Product Specimen Source Codes - Patient     FALSE         FALSE
+#> 5            1 C1578486     patient     patient      Intellectual Product  Disabled Person Code - Patient     FALSE         FALSE
 #> 6            1 C0011847    diabetes    diabetes       Disease or Syndrome                        Diabetes     FALSE         FALSE
 #> 7            1 C0011849    diabetes    diabetes       Disease or Syndrome               Diabetes Mellitus     FALSE         FALSE
 #> 8            1 C2316787 CKD stage 3 ckd stage 3       Disease or Syndrome  Chronic kidney disease stage 3     FALSE         FALSE