minor updates

minor updates

DESCRIPTION

@@ -2,7 +2,7 @@ Package: Characterization
 Type: Package
 Title: Implement Descriptive Studies Using the Common Data Model
 Version: 2.1.2
-Date: 2024-2-20
+Date: 2025-2-20
 Authors@R: c(
 	person("Jenna", "Reps", , "[email protected]", role = c("aut", "cre")),
 	person("Patrick", "Ryan", , "[email protected]", role = c("aut")),

R/AggregateCovariates.R

@@ -26,7 +26,7 @@
 #' @param casePreTargetDuration    The number of days prior to case index we use for FeatureExtraction
 #' @param casePostOutcomeDuration    The number of days prior to case index we use for FeatureExtraction
 #' @param extractNonCaseCovariates Whether to extract aggregate covariates and counts for patients in the targets and outcomes in addition to the cases
-#' @family {Aggregate}
+#' @family Aggregate
 #' @return
 #' A list with the settings
 #'

R/Database.R

@@ -294,14 +294,20 @@ createCharacterizationTables <- function(
     # add database migration here in the future
     migrateDataModel(
       connectionDetails = connectionDetails,
+      connection = conn,
       databaseSchema = resultSchema,
       tablePrefix = tablePrefix
     )
   }
 }
 
 
-migrateDataModel <- function(connectionDetails, databaseSchema, tablePrefix = "") {
+migrateDataModel <- function(
+    connectionDetails,
+    connection,
+    databaseSchema,
+    tablePrefix = ""
+    ) {
   ParallelLogger::logInfo("Migrating data set")
   migrator <- getDataMigrator(
     connectionDetails = connectionDetails,
@@ -319,8 +325,10 @@ migrateDataModel <- function(connectionDetails, databaseSchema, tablePrefix = ""
     dbms = connectionDetails$dbms
   )
 
-  connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
-  on.exit(DatabaseConnector::disconnect(connection))
+  if(missing(connection)){
+    connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
+    on.exit(DatabaseConnector::disconnect(connection))
+  }
   DatabaseConnector::executeSql(connection, updateVersionSql)
 }
 

R/ViewShiny.R

@@ -6,7 +6,7 @@
 #' Input is the output of ...
 #' @param resultFolder   The location of the csv results
 #' @param cohortDefinitionSet  The cohortDefinitionSet extracted using webAPI
-#' @family {Shiny}
+#' @family Shiny
 #'
 #' @return
 #' Opens a shiny app for interactively viewing the results

_pkgdown.yml

@@ -73,3 +73,7 @@ reference:
     desc: >
       Code to run incremetal model
     contents: has_concept("Incremental")
+  - title: "Helpers"
+    desc: >
+      Helper functions such as example data for users
+    contents: has_concept("helper")