fix checks

Author: IoannaNika

DESCRIPTION

@@ -51,7 +51,8 @@ Suggests:
     shiny,
     OhdsiShinyModules,
     rsconnect,
-    yaml
+    yaml,
+    ggplot2
 Remotes:
   ohdsi/OhdsiShinyModules
 License: Apache License

R/ConceptSetUtils.R

@@ -301,7 +301,7 @@ exportConceptSets <- function(cohortDefinitionSet, exportFolder, minCellCount, d
     minCellCount = minCellCount,
     databaseId = databaseId,
     incremental = FALSE,
-    cohortId = conceptSetsExport$cohortId
+    cohortId = cohortDefinitionSet$cohortId
   )
 }
 

R/executeDiagnostics.R

@@ -17,6 +17,8 @@
 #' Get default covariate settings
 #' @description
 #' Default covariate settings for cohort diagnostics execution
+#' 
+#' @return Default covariate settings
 #' @export
 getDefaultCovariateSettings <- function() {
   FeatureExtraction::createTemporalCovariateSettings(
@@ -649,7 +651,7 @@ executeDiagnostics <- function(cohortDefinitionSet,
         minCellCount = minCellCount,
         databaseId = databaseId,
         incremental = FALSE,
-        cohortId = cohorts$cohortId
+        cohortId = cohortDefinitionSet$cohortId
       )
     }
   )

R/plotLogFile.R

@@ -1,5 +1,5 @@
 readLog <- function(path) {
-  df <- read.csv(path, sep = "\t", header = FALSE)
+  df <- utils::read.csv(path, sep = "\t", header = FALSE)
   names(df) <- c("time", "thread", "level", "package", "task", "message")
 
   df %>%

R/runIndexEventBreakdown.R

@@ -270,10 +270,10 @@ runBreakdownIndexEvents <- function(connection,
     return(NULL)
   }
 
-  if (incremental && (nrow(cohorts) - nrow(subset)) > 0) {
+  if (incremental && (nrow(cohortDefinitionSet) - nrow(subset)) > 0) {
     ParallelLogger::logInfo(sprintf(
       "Skipping %s cohorts in incremental mode.",
-      nrow(cohorts) - nrow(subset)
+      nrow(cohortDefinitionSet) - nrow(subset)
     ))
   }