From bf685333d63477107177e1730390c188b46ab170 Mon Sep 17 00:00:00 2001 From: Karandeep Singh Date: Thu, 18 Mar 2021 12:39:24 -0400 Subject: [PATCH] Updated README and pkgdown home page with info on known issues related to the first installation. --- R/clinspacy.R | 4 ++-- README.Rmd | 3 ++- README.md | 9 +++++++-- docs/index.html | 7 ++++--- 4 files changed, 15 insertions(+), 8 deletions(-) diff --git a/R/clinspacy.R b/R/clinspacy.R index a8d6773..21550a6 100644 --- a/R/clinspacy.R +++ b/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 { diff --git a/README.Rmd b/README.Rmd index ff7516a..255b3d1 100644 --- a/README.Rmd +++ b/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. diff --git a/README.md b/README.md index 73b38b8..678c305 100644 --- a/README.md +++ b/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 diff --git a/docs/index.html b/docs/index.html index c4d100f..64cc8a2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -18,7 +18,7 @@ transforms extracted data into a wide format for inclusion in machine learning models. The development of the scispaCy package is described by Neumann (2019) <doi:10.18653/v1/W19-5034>. The medspacy package uses - ConText, an algoritm for determining the context of clinical statements + ConText, an algorithm for determining the context of clinical statements described by Harkema (2009) <doi:10.1016/j.jbi.2009.05.002>. Clinspacy also supports entity embeddings from scispaCy and UMLS cui2vec concept embeddings developed by Beam (2018) <arXiv:1804.01486>."> @@ -112,6 +112,7 @@

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.

 clinspacy_init() # This is optional! The default functionality is to initiatie clinspacy without the UMLS linker
@@ -487,8 +488,8 @@

#> 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