Dev 4.0.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.4.0
+Version: 4.0.0
 Date: 2024-22-10
 Authors@R: c(
     person("Jamie", "Gilbert", email = "gilbert@ohdsi.org", role = c("aut", "cre")),
@@ -55,6 +55,7 @@ Suggests:
     yaml
 Remotes:
   ohdsi/OhdsiShinyModules
+  ohdsi/CohortGenerator@db_cohort_checksums
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics

NEWS.md

@@ -1,3 +1,11 @@
+CohortDiagnostics 4.0.0
+=======================
+
+Change:
+
+1. Created new settings R6 object to allow simplified API and ability to support calling package independently
+
+
 CohortDiagnostics 3.4.0
 =======================
 

R/ConceptSets.R

@@ -667,7 +667,7 @@ runConceptSetDiagnostics <- function(connection,
             }
 
             cohortDefinition <-
-              jsonlite::fromJSON(jsonDef)
+              jsonlite::fromJSON(jsonDef, simplifyDataFrame = FALSE)
 
             primaryCodesetIds <-
               lapply(

R/Private.R

@@ -14,34 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-createIfNotExist <-
-  function(type,
-           name,
-           recursive = TRUE,
-           errorMessage = NULL) {
-    if (is.null(errorMessage) |
-      !is(errorMessage, "AssertColection")) {
-      errorMessage <- checkmate::makeAssertCollection()
-    }
-    if (!is.null(type)) {
-      if (length(name) == 0) {
-        stop(ParallelLogger::logError("Must specify ", name))
-      }
-      if (type %in% c("folder")) {
-        if (!file.exists(gsub("/$", "", name))) {
-          dir.create(name, recursive = recursive)
-          ParallelLogger::logInfo("Created ", type, " at ", name)
-        }
-      }
-      checkmate::assertDirectory(
-        x = name,
-        access = "x",
-        add = errorMessage
-      )
-    }
-    invisible(errorMessage)
-  }
-
 swapColumnContents <-
   function(df,
            column1 = "targetId",