Merge branch 'main' into find_orphan_codes

darwin-eu · Jan 22, 2024 · e82f595 · e82f595
2 parents 44cf1db + 14994c9
commit e82f595
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Showing 24 changed files with 44 additions and 42 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CodelistGenerator
 Title: Generate Code Lists for the OMOP Common Data Model
-Version: 2.1.1
+Version: 2.1.2
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"),
@@ -50,3 +50,4 @@ Config/testthat/parallel: true
 VignetteBuilder: knitr
 URL: https://darwin-eu.github.io/CodelistGenerator/
 Language: en-US
+Config/testthat/parallel: true
diff --git a/R/mockVocabRef.R b/R/mockVocabRef.R
@@ -388,5 +388,4 @@ mockVocabRef <- function(backend = "database") {
   }
 
   cdm
-
 }
diff --git a/extras/precomputeVignetteData.R b/extras/precomputeVignetteData.R
@@ -14,7 +14,7 @@ devtools::load_all()
 
 # example with postgres database connection details
 db <- dbConnect(RPostgres::Postgres(),
-                dbname = "cdm_iqvia_pharmetrics_plus_202203",
+                dbname = "cdm_gold_202301",
                 port = Sys.getenv("DB_PORT") ,
                 host = "163.1.65.51",
                 user = Sys.getenv("DB_USER"),
@@ -46,9 +46,9 @@ rm(cdm)
 # intro vignette ----
 vocabVersion <- getVocabVersion(cdm = cdm_arrow)
 
-saveRDS(
+save(
   vocabVersion,
-  here("vignettes", "introVocab.RData")
+  file = here("vignettes", "introVocab.RData")
 )
 
 
@@ -70,12 +70,12 @@ saveRDS(
 dementiaCodes1 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "dementia",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = FALSE,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = FALSE,
   exclude = NULL,
   includeDescendants = TRUE,
   includeAncestor = FALSE,
-  verbose=TRUE
+  #verbose=TRUE
 )
 saveRDS(
   dementiaCodes1,
@@ -112,15 +112,15 @@ saveRDS(
 oaCodes1 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = FALSE,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = FALSE,
   exclude = c(
     "post-infection",
     "post-traumatic"
   ),
   includeDescendants = FALSE,
   includeAncestor = FALSE,
-  verbose = TRUE
+  #verbose = TRUE
 )
 saveRDS(
   oaCodes1,
@@ -131,8 +131,8 @@ saveRDS(
 oaCodes2 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = FALSE,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = FALSE,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -149,9 +149,9 @@ saveRDS(
 oaCodes3 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = c("Condition", "Observation"),
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = FALSE,
-  maxDistanceCost = 0.1,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = FALSE,
+  #maxDistanceCost = 0.1,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -169,9 +169,9 @@ oaCodes4 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
   searchInSynonyms = TRUE,
-  searchViaSynonyms = TRUE,
-  fuzzyMatch = FALSE,
-  maxDistanceCost = 0.1,
+  #searchViaSynonyms = TRUE,
+  #fuzzyMatch = FALSE,
+  #maxDistanceCost = 0.1,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -201,15 +201,13 @@ saveRDS(
   here("vignettes", "optionsData04.RData")
 )
 
-
-
 # fuzzy search
 oaCodes6 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = TRUE,
-  maxDistanceCost = 0.1,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = TRUE,
+  #maxDistanceCost = 0.1,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -226,9 +224,9 @@ saveRDS(
 oaCodes7 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = TRUE,
-  maxDistanceCost = 0.2,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = TRUE,
+  #maxDistanceCost = 0.2,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -245,9 +243,9 @@ saveRDS(
 oaCodes8 <- getCandidateCodes(cdm = cdm_arrow,
   keywords = "osteoarthritis",
   domains = "Condition",
-  searchViaSynonyms = FALSE,
-  fuzzyMatch = FALSE,
-  maxDistanceCost = 0.2,
+  #searchViaSynonyms = FALSE,
+  #fuzzyMatch = FALSE,
+  #maxDistanceCost = 0.2,
   exclude = c(
     "post-infection",
     "post-traumatic"
@@ -265,8 +263,7 @@ ac_codes_1 <- getCandidateCodes(cdm = cdm_arrow,
                                      keywords="acetaminophen",
                                      domains="drug",
                                      standardConcept="standard",
-                                     includeDescendants = TRUE,
-                                     verbose = TRUE)
+                                     includeDescendants = TRUE)
 saveRDS(
   ac_codes_1,
   here("vignettes", "medData01.RData")
@@ -277,8 +274,7 @@ ac_codes_2a <- getCandidateCodes(cdm = cdm_arrow,
                                              "acetaminophen intravenous"),
                                  domains="drug",
                                  standardConcept="standard",
-                                 includeDescendants = TRUE,
-                                 verbose = TRUE)
+                                 includeDescendants = TRUE)
 saveRDS(
   ac_codes_2a,
   here("vignettes", "medData02a.RData")
@@ -287,10 +283,9 @@ saveRDS(
 ac_codes_2b <- getCandidateCodes(cdm = cdm_arrow,
                                 keywords="acetaminophen",
                                 domains="drug",
-                                doseForm = c("injection", "intravenous"),
+                                #doseForm = c("injection", "intravenous"),
                                 standardConcept="standard",
-                                includeDescendants = TRUE,
-                                verbose = TRUE )
+                                includeDescendants = TRUE)
 saveRDS(
   ac_codes_2b,
   here("vignettes", "medData02b.RData")
@@ -305,11 +300,10 @@ c <- compareCodelists(ac_codes_2, ac_codes_2a)
 ac_codes_3 <- getCandidateCodes(cdm = cdm_arrow,
                                 keywords="acetaminophen",
                                 domains="drug",
-                                conceptClassId = c("Quant Clinical Drug"),
-                                doseForm = c("injection", "intravenous"),
+                                #conceptClassId = c("Quant Clinical Drug"),
+                                #doseForm = c("injection", "intravenous"),
                                 standardConcept="standard",
-                                includeDescendants = TRUE,
-                                verbose = TRUE)
+                                includeDescendants = TRUE)
 saveRDS(
   ac_codes_3,
   here("vignettes", "medData03.RData")

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,3 +1,11 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
 library(testthat)
 library(CodelistGenerator)
 

diff --git a/vignettes/a01_Introduction_to_CodelistGenerator.Rmd b/vignettes/a01_Introduction_to_CodelistGenerator.Rmd
@@ -60,7 +60,7 @@ getVocabVersion(cdm = cdm)
 ```
 
 ```{r,  message=FALSE, warning=FALSE,echo=FALSE}
-vocabVersion <- readRDS(here("vignettes", "introVocab.RData"))
+vocabVersion <- load(here("vignettes", "introVocab.RData"))
 vocabVersion
 ```
 

diff --git a/vignettes/introData01.RData b/vignettes/introData01.RData
diff --git a/vignettes/introData02.RData b/vignettes/introData02.RData
diff --git a/vignettes/introData03.RData b/vignettes/introData03.RData
diff --git a/vignettes/introData04.RData b/vignettes/introData04.RData
diff --git a/vignettes/introData05.RData b/vignettes/introData05.RData
diff --git a/vignettes/introVocab.RData b/vignettes/introVocab.RData
diff --git a/vignettes/medData01.RData b/vignettes/medData01.RData
diff --git a/vignettes/medData02a.RData b/vignettes/medData02a.RData
diff --git a/vignettes/medData02b.RData b/vignettes/medData02b.RData
diff --git a/vignettes/medData03.RData b/vignettes/medData03.RData
diff --git a/vignettes/medDataConceptClass.RData b/vignettes/medDataConceptClass.RData
diff --git a/vignettes/medDataDoseForms.RData b/vignettes/medDataDoseForms.RData
diff --git a/vignettes/optionsData01.RData b/vignettes/optionsData01.RData
diff --git a/vignettes/optionsData02.RData b/vignettes/optionsData02.RData
diff --git a/vignettes/optionsData03.RData b/vignettes/optionsData03.RData
diff --git a/vignettes/optionsData04.RData b/vignettes/optionsData04.RData
diff --git a/vignettes/optionsData05.RData b/vignettes/optionsData05.RData
diff --git a/vignettes/optionsData06.RData b/vignettes/optionsData06.RData
diff --git a/vignettes/optionsData07.RData b/vignettes/optionsData07.RData
Original file line number	Diff line number	Diff line change
Expand Up		@@ -388,5 +388,4 @@ mockVocabRef <- function(backend = "database") {
		}

		cdm

		}