Merge pull request #151 from darwin-eu/v3.0

V3.0
darwin-eu · May 31, 2024 · 647ea79 · 647ea79
2 parents f7406d1 + 65c109e
commit 647ea79
Show file tree

Hide file tree

Showing 19 changed files with 69 additions and 31 deletions.
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -30,7 +30,7 @@ devtools::test()
 Code to add new functionality should be accompanied by tests. Code coverage can be checked using: 
 ``` r
 # note, you may first have to detach the package
-# detach("package:IncidencePrevalence", unload=TRUE)
+# detach("package:CodelistGenerator", unload=TRUE)
 devtools::test_coverage()
 ```
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CodelistGenerator
 Title: Identify Relevant Clinical Codes and Evaluate Their Use
-Version: 2.2.3.900
+Version: 3.0
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"),
@@ -32,7 +32,7 @@ Imports:
     cli (>= 3.1.0),
     purrr,
     lubridate,
-    PatientProfiles (>= 0.6.0),
+    PatientProfiles (>= 1.0.0),
     RJSONIO,
     vctrs,
     visOmopResults (>= 0.3.0),
@@ -50,10 +50,6 @@ Suggests:
     tibble,
     gt,
     flextable
-Remotes: 
-    darwin-eu-dev/omopgenerics,
-    darwin-eu/CDMConnector,
-    darwin-eu/visOmopResults
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,7 @@
-# CodelistGenerator 2.2.3.900 (development version)
+# CodelistGenerator 3.0
 * Add function getRelationshipId 
 * Add functions summariseAchillesCodeUse (replaces achillesCodeUse), summariseOrphanCodes (replaces findOrphanCodes), tableAchillesCodeUse, tableCodeUse, tableCohortCodeUse, tableOrphanCodes.
 
-
 # CodelistGenerator 2.2.3
 * Fix for forthcoming breaking change in dependency omopgenerics
 

diff --git a/R/checks.R b/R/checks.R
@@ -1,4 +1,4 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of CodelistGenerator
 #

diff --git a/R/codesFromConceptSet.R b/R/codesFromConceptSet.R
@@ -1,4 +1,4 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of CodelistGenerator
 #
@@ -364,12 +364,17 @@ formatConceptList <- function(cdm, conceptListTable) {
           "descendant_concept_id"
         ) %>%
         dplyr::mutate(concept_id = as.integer(.data$concept_id)) %>%
-        dplyr::inner_join(
+        dplyr::right_join(
           cdm[[conceptListTable]] %>%
             dplyr::mutate(concept_id = as.integer(.data$concept_id)) %>%
             dplyr::filter(.data$include_descendants == TRUE),
           by = "concept_id"
         ) %>%
+        dplyr::mutate(descendant_concept_id = dplyr::if_else(
+          # in case concept is not in ancestor table
+          # (even though it should be)
+          is.na(.data$descendant_concept_id),
+          .data$concept_id, .data$descendant_concept_id)) %>%
         dplyr::select(-"concept_id") %>%
         dplyr::rename("concept_id" = "descendant_concept_id")
     ) %>%

diff --git a/R/codesInUse.R b/R/codesInUse.R
@@ -1,4 +1,4 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of CodelistGenerator
 #

diff --git a/R/compareCodelists.R b/R/compareCodelists.R
@@ -1,6 +1,6 @@
 # Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/drugCodes.R b/R/drugCodes.R
@@ -1,6 +1,6 @@
 # Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/getCandidateCodes.R b/R/getCandidateCodes.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/getMappings.R b/R/getMappings.R
@@ -1,6 +1,6 @@
 # Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/inputValidation.R b/R/inputValidation.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/mockVocabRef.R b/R/mockVocabRef.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/runSearch.R b/R/runSearch.R
@@ -1,6 +1,6 @@
 # Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/summariseCodeUse.R b/R/summariseCodeUse.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/R/vocabUtilities.R b/R/vocabUtilities.R
@@ -1,6 +1,6 @@
-# Copyright 2024 DARWIN EU (C)
+# Copyright 2024 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CodelistGenerator
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -403,7 +403,6 @@ getDescendantsAndAncestor <- function(cdm, conceptId, ingredientRange, doseForm)
     dplyr::left_join(cdm$concept,
                      by = "concept_id") %>%
     dplyr::compute()
-  CDMConnector::dropTable(cdm, conceptIdDbTable)
 
   descendants <- addIngredientCount(cdm = cdm, concepts = descendants) %>%
     dplyr::filter(.data$ingredient_count >= !!ingredientRange[1],
@@ -456,6 +455,8 @@ descendants$ancestor_concept_id <- stringr::str_replace_all(
                                      doseForm = doseForm)
   }
 
+  CDMConnector::dropTable(cdm, conceptIdDbTable)
+
   # nb conceptId will also be a descendant of itself
   return(descendants)
 
@@ -520,7 +521,7 @@ addIngredientCount <- function(cdm, concepts) {
                         dplyr::select("concept_id"),
                by = c("ancestor_concept_id" = "concept_id"))
 
- ingredient_count <- concepts%>%
+ ingredient_count <- concepts %>%
    dplyr::select("concept_id") %>%
    dplyr::distinct() %>%
    dplyr::left_join(ingredient_ancestor,

diff --git a/inst/concepts_dbms/oa_desc.json b/inst/concepts_dbms/oa_desc.json
@@ -0,0 +1,12 @@
+{
+  "items": [
+    {
+      "concept": {
+        "CONCEPT_ID": 4079750
+      },
+      "isExcluded": false,
+      "includeDescendants": true,
+      "includeMapped": false
+    }
+  ]
+}
diff --git a/inst/concepts_dbms/oa_no_desc.json b/inst/concepts_dbms/oa_no_desc.json
@@ -0,0 +1,12 @@
+{
+  "items": [
+    {
+      "concept": {
+        "CONCEPT_ID": 4079750
+      },
+      "isExcluded": false,
+      "includeDescendants": false,
+      "includeMapped": false
+    }
+  ]
+}
diff --git a/tests/testthat/test-dbms.R b/tests/testthat/test-dbms.R
@@ -15,6 +15,9 @@ test_that("redshift", {
                                     cdm_schema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
                                     write_schema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA"))
 
+  cdm$concept <- cdm$concept |>
+    dplyr::mutate(concept_id = as.integer64(concept_id)) |>
+    dplyr::compute()
 
   # candidate code search
   expect_no_error(asthma<-getCandidateCodes(cdm,
@@ -122,6 +125,16 @@ test_that("redshift", {
                                cdm = cdm,
                                countBy = "not an option"))
 
+  # working concept set example with mock
+  x <- codesFromConceptSet(
+    cdm = cdm, path =  system.file(package = "CodelistGenerator",
+                                   "concepts_dbms")
+  )
+  expect_true(x$oa_no_desc == 4079750)
+  expect_true(!761485 %in% x$oa_no_desc)
+  expect_true(761485 %in% x$oa_desc)
+
+
   CDMConnector::cdm_disconnect(cdm)
 })