Merge pull request #1042 from OHDSI/develop

Release version 3.2.0
OHDSI · Apr 4, 2023 · 0e3764f · 0e3764f
2 parents 21d6eb3 + 7caa095
commit 0e3764f
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diff --git a/.github/workflows/R_CMD_check_Hades_minor.yml b/.github/workflows/R_CMD_check_Hades_minor.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.1.2
+Version: 3.2.0
 Date: 2022-12-19
 Authors@R: c(
     person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
@@ -38,42 +38,33 @@ Imports:
   SqlRender (>= 1.9.0),
   stringr,
   tidyr (>= 1.2.0),
-  CohortGenerator (>= 0.5.0)
+  CohortGenerator (>= 0.8.0),
+  remotes
 Suggests:
-  CirceR,
-  DT,
   Eunomia,
-  ggplot2,
-  htmltools,
-  knitr,
-  lubridate,
-  pool,
-  plotly,
-  purrr,
-  RColorBrewer,
-  remotes,
-  rmarkdown,
   ROhdsiWebApi (>= 1.2.0),
   RSQLite (>= 2.2.1),
   scales,
-  shiny,
-  shinydashboard,
-  shinyWidgets,
   testthat,
   withr,
-  zip
+  zip,
+  knitr,
+  shiny,
+  OhdsiShinyModules
 Remotes:
   ohdsi/Eunomia,
   ohdsi/FeatureExtraction,
   ohdsi/ResultModelManager,
   ohdsi/ROhdsiWebApi,
   ohdsi/CirceR,
-  ohdsi/CohortGenerator
+  ohdsi/CohortGenerator,
+  ohdsi/OhdsiShinyModules
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics
 BugReports: https://github.com/OHDSI/CohortDiagnostics/issues
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 Language: en-US
 StagedInstall: no
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,10 +16,10 @@ export(runCohortRelationshipDiagnostics)
 export(runCohortTimeSeriesDiagnostics)
 export(uploadResults)
 import(DatabaseConnector)
-import(dplyr)
 importFrom(CohortGenerator,getCohortTableNames)
 importFrom(FeatureExtraction,createDefaultCovariateSettings)
 importFrom(FeatureExtraction,createTemporalCovariateSettings)
+importFrom(dplyr,"%>%")
 importFrom(grDevices,rgb)
 importFrom(methods,is)
 importFrom(rlang,.data)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+CohortDiagnostics 3.2.0
+=======================
+
+1. Do not run orphan concepts checks for any subset cohorts
+
+2. Remove use of lookback period for IR calculations - this is now a setting of the call to the package
+
+3. Added data migration to support subsets in database schema (allow future functionality to take care of them)
+
+4. Added functionality to `launchDiagnosticsExplorer` to make publishing to poist connect/shinyapps.io more straightforward (still requires removal of ggiraph)
+
+5. Moved most shiny code to `OHDSI/OhdsiShinyModules`
+
+
 CohortDiagnostics 3.1.2
 =======================
 Bug Fixes:

diff --git a/R/CohortCharacterizationDiagnostics.R b/R/CohortCharacterizationDiagnostics.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #
@@ -65,7 +65,7 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
     results$covariateRef <- featureExtractionOutput$covariateRef
   } else {
     covariateIds <- results$covariateRef %>%
-      dplyr::select(covariateId)
+      dplyr::select("covariateId")
     Andromeda::appendToTable(
       results$covariateRef,
       featureExtractionOutput$covariateRef %>%
@@ -80,7 +80,7 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
   if ("covariates" %in% names(featureExtractionOutput) &&
     dplyr::pull(dplyr::count(featureExtractionOutput$covariates)) > 0) {
     covariates <- featureExtractionOutput$covariates %>%
-      dplyr::rename(cohortId = cohortDefinitionId) %>%
+      dplyr::rename("cohortId" = "cohortDefinitionId") %>%
       dplyr::left_join(populationSize, by = "cohortId", copy = TRUE) %>%
       dplyr::mutate(p = sumValue / populationSize)
 
@@ -98,18 +98,18 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
     covariates <- covariates %>%
       dplyr::mutate(sd = sqrt(p * (1 - p))) %>%
       dplyr::select(-p) %>%
-      dplyr::rename(mean = averageValue) %>%
+      dplyr::rename("mean" = "averageValue") %>%
       dplyr::select(-populationSize)
 
     if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) {
       covariates <- covariates %>%
         dplyr::select(
-          cohortId,
-          timeId,
-          covariateId,
-          sumValue,
-          mean,
-          sd
+          "cohortId",
+          "timeId",
+          "covariateId",
+          "sumValue",
+          "mean",
+          "sd"
         )
       if (length(is.na(covariates$timeId)) > 0) {
         covariates[is.na(covariates$timeId), ]$timeId <- -1
@@ -118,12 +118,12 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       covariates <- covariates %>%
         dplyr::mutate(timeId = 0) %>%
         dplyr::select(
-          cohortId,
-          timeId,
-          covariateId,
-          sumValue,
-          mean,
-          sd
+          "cohortId",
+          "timeId",
+          "covariateId",
+          "sumValue",
+          "mean",
+          "sd"
         )
     }
     if ("covariates" %in% names(results)) {
@@ -146,12 +146,12 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       covariates <- covariates %>%
         dplyr::mutate(sumValue = -1) %>%
         dplyr::select(
-          cohortId,
-          timeId,
-          covariateId,
-          sumValue,
-          mean,
-          sd
+          "cohortId",
+          "timeId",
+          "covariateId",
+          "sumValue",
+          "mean",
+          "sd"
         )
       if (length(is.na(covariates$timeId)) > 0) {
         covariates[is.na(covariates$timeId), ]$timeId <- -1
@@ -163,12 +163,12 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           timeId = 0
         ) %>%
         dplyr::select(
-          cohortId,
-          timeId,
-          covariateId,
-          sumValue,
-          mean,
-          sd
+          "cohortId",
+          "timeId",
+          "covariateId",
+          "sumValue",
+          "mean",
+          "sd"
         )
     }
     if ("covariates" %in% names(results)) {

diff --git a/R/CohortDiagnostics.R b/R/CohortDiagnostics.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #
@@ -21,7 +21,7 @@
 #' @importFrom grDevices rgb
 #' @importFrom stats aggregate
 #' @importFrom utils write.csv install.packages menu unzip setTxtProgressBar txtProgressBar packageName
-#' @import dplyr
+#' @importFrom dplyr %>%
 #' @importFrom rlang .data
 #' @importFrom methods is
 #' @importFrom FeatureExtraction createDefaultCovariateSettings createTemporalCovariateSettings

diff --git a/R/CohortLevelDiagnostics.R b/R/CohortLevelDiagnostics.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/CohortRelationship.R b/R/CohortRelationship.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/ConceptIds.R b/R/ConceptIds.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #