v1.0.8

darwin-eu · Sep 10, 2024 · 8f7f3aa · 8f7f3aa
1 parent 3b3334e
commit 8f7f3aa
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.4
-Date: 2024-03-18 09:13:46 UTC
-SHA: 5d055fdc24e44e04a2c42497b092dbff1cb9ade0
+Version: 1.0.8
+Date: 2024-09-10 07:20:12 UTC
+SHA: 57b01591dca6ce7ff32929d541d6895f74e99688
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DrugExposureDiagnostics
 Title: Diagnostics for OMOP Common Data Model Drug Records
-Version: 1.0.7
+Version: 1.0.8
 Authors@R: c(
     person("Ger", "Inberg", email = "g.inberg@erasmusmc.nl", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8993-8748")),
@@ -24,7 +24,7 @@ Description: Ingredient specific diagnostics for drug exposure records in the Ob
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.0)
 Imports: 
@@ -51,7 +51,6 @@ Suggests:
     DT,
     graphics,
     SqlRender,
-    PaRe,
     magick,
     DiagrammeRsvg,
     ggplot2,

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,8 @@
 # DrugExposureDiagnostics (development version)
 
+# DrugExposureDiagnostics 1.0.8
+* Skip unavailable concepts (#253 and #254)
+
 # DrugExposureDiagnostics 1.0.7
 * Updates related to newest release of DrugUtilisation
 

diff --git a/R/executeChecks.R b/R/executeChecks.R
@@ -77,18 +77,24 @@ executeChecks <- function(cdm,
   resultList <- vector(mode = "list", length = length(ingredients))
   for (i in seq_along(ingredients)) {
     ingredient <- ingredients[i]
-    resultList[[i]] <- executeChecksSingleIngredient(cdm = cdm,
-                                                     ingredient = ingredient,
-                                                     subsetToConceptId = subsetToConceptId,
-                                                     checks = checks,
-                                                     minCellCount = minCellCount,
-                                                     sampleSize = sample,
-                                                     tablePrefix = tablePrefix,
-                                                     earliestStartDate = earliestStartDate,
-                                                     verbose = verbose,
-                                                     byConcept = byConcept)
+    ingredientResult <- NULL
+    tryCatch({
+      ingredientResult <- executeChecksSingleIngredient(cdm = cdm,
+                                                        ingredient = ingredient,
+                                                        subsetToConceptId = subsetToConceptId,
+                                                        checks = checks,
+                                                        minCellCount = minCellCount,
+                                                        sampleSize = sample,
+                                                        tablePrefix = tablePrefix,
+                                                        earliestStartDate = earliestStartDate,
+                                                        verbose = verbose,
+                                                        byConcept = byConcept)
+    }, error = function(e) {
+      warning(e)
+    })
+    resultList[[i]] <- ingredientResult
   }
-  resultList <- do.call(Map, c(f = rbind, resultList))
+  resultList <- do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))
   return(resultList)
 }
 

diff --git a/R/ingredientDescendantsInDb.R b/R/ingredientDescendantsInDb.R
@@ -41,7 +41,6 @@ ingredientDescendantsInDb <- function(cdm,
     messageStore = errorMessage
   )
   checkLogical(verbose, messageStore = errorMessage)
-  checkIsIngredient(cdm = cdm, conceptId = ingredient, messageStore = errorMessage)
   checkIngredientInTable(cdm = cdm, conceptId = ingredient, tableName = "drug_strength", messageStore = errorMessage)
   checkmate::reportAssertions(collection = errorMessage)
 

diff --git a/R/mockDrugExposure.R b/R/mockDrugExposure.R
@@ -75,7 +75,6 @@ mockDrugExposure <- function(drug_exposure = NULL,
     min_levels_of_separation <- as.integer(rep(0, each = 6))
     max_levels_of_separation <- as.integer(rep(1, each = 6))
 
-
     concept_ancestor <-
       data.frame(
         ancestor_concept_id = ancestor_concept_id ,
@@ -114,11 +113,11 @@ mockDrugExposure <- function(drug_exposure = NULL,
           "Oral Tablet",
           "METAMIZOLE"
         ) ,
-        domain_id = c(rep("Drug", 7),"Route","Type Concept",rep("Drug",2)),
-        vocabulary_id = c(rep("RxNorm", 7), "SNOMED","Drug Type","RxNorm","RxNormExtension"),
-        concept_class_id = c("Ingredient", rep("Clinical Drug", 6),"Qualifier Value","Drug Type","Dose Form","Ingredient"),
+        domain_id = c(rep("Drug", 7), "Route", "Type Concept", rep("Drug",2)),
+        vocabulary_id = c(rep("RxNorm", 7), "SNOMED", "Drug Type", "RxNorm", "RxNormExtension"),
+        concept_class_id = c("Ingredient", rep("Clinical Drug", 6), "Qualifier Value", "Drug Type", "Dose Form", "Ingredient"),
         standard_concept = c(rep("S", 8), rep("Non-standard",2), "S"),
-        concept_code = c("161", "313782", "833036", "1049221", "1043400", "857005", "282464","26643006","OMOP4822241","421026006","OMOP5172468"),
+        concept_code = c("161", "313782", "833036", "1049221", "1043400", "857005", "282464", "26643006", "OMOP4822241", "421026006", "OMOP5172468"),
         valid_start_date = c(rep(as.Date("1970-01-01"), 11)),
         valid_end_date = c(rep(as.Date("2099-12-31"), 11)),
         invalid_reason = as.character(c(rep(NA, 11)))
@@ -136,7 +135,7 @@ mockDrugExposure <- function(drug_exposure = NULL,
   }
 
   if (is.null(drug_strength)) {
-    ancestor_concept_id <- c(rep(1125315, 6),36854851)
+    ancestor_concept_id <- c(rep(1125315, 6), 36854851)
     descendant_concept_id <-
       c(40162522, 1127078, 1127433, 40229134, 40231925, 19133768,NA)
 

diff --git a/tests/testthat/test-executeChecks.R b/tests/testthat/test-executeChecks.R
@@ -259,3 +259,14 @@ test_that("empty drug_strength table gives an error", {
   DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
 })
 
+test_that("results from multiple ingredients should be joined also if there is one in between that doesn't exist", {
+  cdm <- mockDrugExposure()
+
+  result <- executeChecks(cdm = cdm,
+                          ingredients = c(1125315, 36854851, 1125315))
+  # should have 2 times result for 1125315
+  summary <- result$conceptSummary
+  expect_equal(nrow(summary), 12)
+
+  DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+})