Revert to using null in shell settings

R/checkColumn.R

@@ -16,33 +16,33 @@
 #' testSettings$filters[[1]]<-list(value_col="RACE",label="Race")
 #' testSettings$filters[[2]]<-list(value_col=NULL,label="No Column")
 #' testSettings$filters[[3]]<-list(value_col="NotAColumn",label="Invalid Column")
-#' 
+#'
 #' #pass ($valid == TRUE)
 #' safetyGraphics:::checkColumn(key=list("id_col"),
-#'                                     settings=testSettings, adlbc) 
-#'                                     
+#'                                     settings=testSettings, adlbc)
+#'
 #' #pass
 #' safetyGraphics:::checkColumn(key=list("filters",1,"value_col"),
-#'                                     settings=testSettings, adlbc) 
-#'                                     
+#'                                     settings=testSettings, adlbc)
+#'
 #' #NULL column pass
 #' safetyGraphics:::checkColumn(key=list("filters",2,"value_col"),
-#'                                     settings=testSettings, adlbc) 
-#'                                     
+#'                                     settings=testSettings, adlbc)
+#'
 #' #invalid column fails
 #' safetyGraphics:::checkColumn(key=list("filters",3,"value_col"),
-#'                                     settings=testSettings, adlbc) 
+#'                                     settings=testSettings, adlbc)
 #' @keywords internal
 
 checkColumn <- function(key, settings, data){
   stopifnot(typeof(key)=="list",typeof(settings)=="list")
-  
+
   current <- list(key=key)
   current$text_key <-  paste( unlist(current$key), collapse='--')
   current$type <- "column"
   current$description <- "column parameter from setting setting found in data?"
   current$value <- getSettingValue(key=key,settings=settings)
-  if(is.na(current$value)||is.null(current$value)){
+  if(is.null(current$value)){
     current$value <- "--No Value Given--"
     current$valid <- TRUE
     current$message <- ""

R/checkNumeric.R

@@ -10,11 +10,11 @@
 #' @examples
 #' testSettings<-generateSettings(standard="AdAM")
 #' #pass ($valid == FALSE)
-#' safetyGraphics:::checkNumeric(key=list("id_col"),settings=testSettings, data=adlbc) 
-#' 
+#' safetyGraphics:::checkNumeric(key=list("id_col"),settings=testSettings, data=adlbc)
+#'
 #' #pass ($valid == TRUE)
-#' safetyGraphics:::checkNumeric(key=list("value_col"),settings=testSettings, data=adlbc) 
-#' 
+#' safetyGraphics:::checkNumeric(key=list("value_col"),settings=testSettings, data=adlbc)
+#'
 #' @keywords internal
 
 checkNumeric <- function(key, settings, data){
@@ -25,7 +25,7 @@ checkNumeric <- function(key, settings, data){
   current$type <- "numeric"
   current$description <- "specified column is numeric?"
   current$value <- getSettingValue(key=key,settings=settings)
-  if(is.na(current$value)||is.null(current$value)){
+  if(is.null(current$value)){
     current$value <- "--No Value Given--"
     current$valid <- TRUE
     current$message <- ""

R/generateSettings.R

@@ -1,94 +1,94 @@
 #' Generate a settings object based on a data standard
 #'
-#' This function returns a settings object for the eDish chart based on the specified data standard. 
+#' This function returns a settings object for the eDish chart based on the specified data standard.
 #'
 #' The function is designed to work with the SDTM and AdAM CDISC(<https://www.cdisc.org/>) standards for clinical trial data. Currently, eDish is the only chart supported.
 #'
 #' @param standard The data standard for which to create settings. Valid options are "SDTM", "AdAM" or "None". Default: \code{"None"}.
 #' @param charts The chart or chart(s) for which settings should be generated. Default: \code{NULL} (uses all available charts).
-#' @param useDefaults Specifies whether default values from settingsMetadata should be included in the settings object. Default: \code{TRUE}. 
+#' @param useDefaults Specifies whether default values from settingsMetadata should be included in the settings object. Default: \code{TRUE}.
 #' @param partial Boolean for whether or not the standard is a partial standard. Default: \code{FALSE}.
 #' @param partial_keys Optional character vector of the matched settings if partial is TRUE. Settings should be identified using the text_key format described in ?settingsMetadata. Setting is ignored when partial is FALSE. Default: \code{NULL}.
-#' @param custom_settings a tibble with text_key and customValue columns specifiying customizations to be applied to the settings object. Default: \code{NULL}. 
+#' @param custom_settings a tibble with text_key and customValue columns specifiying customizations to be applied to the settings object. Default: \code{NULL}.
 #' @return A list containing the appropriate settings for the selected chart
-#' 
-#' @examples 
-#' 
-#' generateSettings(standard="SDTM") 
+#'
+#' @examples
+#'
+#' generateSettings(standard="SDTM")
 #' generateSettings(standard="SdTm") #also ok
 #' generateSettings(standard="ADaM")
 #' pkeys<- c("id_col","measure_col","value_col")
 #' generateSettings(standard="adam", partial=TRUE, partial_keys=pkeys)
-#' 
-#' generateSettings(standard="a different standard") 
+#'
+#' generateSettings(standard="a different standard")
 #' #returns shell settings list with no data mapping
-#' 
+#'
 #' \dontrun{
-#' generateSettings(standard="adam",chart="AEExplorer") #Throws error. Only eDish supported so far. 
+#' generateSettings(standard="adam",chart="AEExplorer") #Throws error. Only eDish supported so far.
 #' }
-#' 
+#'
 #' @importFrom dplyr "filter" full_join
 #' @importFrom stringr str_split
 #' @importFrom rlang .data
-#' 
+#'
 #' @export
 
 generateSettings <- function(standard="None", charts=NULL, useDefaults=TRUE, partial=FALSE, partial_keys=NULL, custom_settings=NULL){
-  
+
   # Check that partial_keys is supplied if partial is true
   if  (is.null(partial_keys) & partial ) {
     stop("partial_keys must be supplied if the standard is partial")
   }
-  
+
   # Coerce options to lowercase
   standard<-tolower(standard)
   if(!is.null(charts)){
-    charts<-tolower(charts)  
+    charts<-tolower(charts)
   }
-  
+
   #############################################################################
-  # get keys & default values for settings using a data standard (data and field mappings) 
+  # get keys & default values for settings using a data standard (data and field mappings)
   ############################################################################
   # Build a table of data mappings for the selected standard and partial settings
   standardList<-safetyGraphics::standardsMetadata%>%select(-.data$text_key)%>%names
-  
+
   if(standard %in% standardList){
     dataDefaults <- safetyGraphics::getSettingsMetadata(
-      charts = charts, 
+      charts = charts,
       cols=c("text_key",standard,"setting_required")
-    ) %>% 
+    ) %>%
     filter(.data$setting_required)%>%
-    select(-.data$setting_required)%>%  
+    select(-.data$setting_required)%>%
     rename("dataDefault" = standard)%>%
     filter(.data$dataDefault != '')
   }else{
     dataDefaults<-tibble(text_key=character(),dataDefault=character(), .rows=0)
   }
-  
+
   if(partial){
-    dataDefaults <-dataDefaults%>%filter(.data$text_key %in% partial_keys) 
+    dataDefaults <-dataDefaults%>%filter(.data$text_key %in% partial_keys)
   }
-  
+
   #############################################################################
-  # get keys & default values for settings not using a data standard  
+  # get keys & default values for settings not using a data standard
   #############################################################################
   if(useDefaults){
     otherDefaults <- safetyGraphics::getSettingsMetadata(
-      charts = charts, 
+      charts = charts,
       filter = !.data$column_mapping & !.data$field_mapping,
       cols=c("text_key","default")
     )%>%
     rename("otherDefault"="default")
   }else{
     otherDefaults <- tibble(text_key=character(),otherDefault=character(), .rows=0)
   }
-  
+
   #############################################################################
   # merge all keys & default values
   #############################################################################
   key_values <- full_join(dataDefaults, otherDefaults, by="text_key")
   key_values <- key_values %>% mutate(default=ifelse(is.na(.data$dataDefault),.data$otherDefault,.data$dataDefault))
-  
+
   #############################################################################
   # Apply custom settings (if any)
   #############################################################################
@@ -97,24 +97,24 @@ generateSettings <- function(standard="None", charts=NULL, useDefaults=TRUE, par
   } else {
     key_values$customValue<-NA
   }
-  
+
   key_values<-key_values %>% mutate(value=ifelse(is.na(.data$customValue), .data$default, .data$customValue))
-  
+
   #############################################################################
   # create shell settings object
   #############################################################################
-  shell<-generateShell(charts=charts) 
-  
+  shell<-generateShell(charts=charts)
+
   #########################################################################################
   # populate the shell settings by looping through key_values and apply them to the shell
   #########################################################################################
   for(row in 1:nrow(key_values)){
     shell<-setSettingsValue(
-      settings = shell, 
-      key = textKeysToList(key_values[row,"text_key"])[[1]], 
+      settings = shell,
+      key = textKeysToList(key_values[row,"text_key"])[[1]],
       value = key_values[row, "value"][[1]]
     )
-  }    
-  
+  }
+
   return(shell)
 }

R/generateShell.R

@@ -24,7 +24,7 @@ generateShell <- function(charts=NULL){
   for (i in 1:length(keys) ) {
     shell<-setSettingsValue(
       key=keys[[i]],
-      value=NA, #NA is prefered here since NULL deletes the element in the list
+      value=NULL, 
       settings=shell,
       forceCreate=TRUE
     )

R/setSettingsValue.R

@@ -34,7 +34,11 @@ setSettingsValue <- function(key, value, settings, forceCreate=FALSE){
 
   firstKey <- key[[1]]
   if(length(key)==1){
-    settings[[firstKey]]<-value
+    if(is.null(value)){
+      settings[firstKey]<-list(NULL)
+    }else{
+      settings[[firstKey]]<-value
+    }
     return(settings)
   }else{
     settings[[firstKey]]<-setSettingsValue(settings = settings[[firstKey]],key = key[2:length(key)], value=value, forceCreate=forceCreate)

R/trimData.R

@@ -22,10 +22,10 @@ trimData <- function(data, settings, chart="edish"){
 
   ## Remove columns not in settings ##
   col_names <- colnames(data)
-  
+
   allKeys <- getSettingsMetadata(charts=chart, filter_expr = .data$column_mapping, cols = c("text_key","setting_type"))
   dataKeys <- allKeys %>% filter(.data$setting_type !="vector") %>% pull(.data$text_key) %>% textKeysToList()
-  
+
   # Add items in vectors to list individually
   dataVectorKeys <- allKeys %>% filter(.data$setting_type =="vector") %>% pull(.data$text_key) %>% textKeysToList()
   for(key in dataVectorKeys){
@@ -37,12 +37,12 @@ trimData <- function(data, settings, chart="edish"){
         sub <- current[[i]]
         if(typeof(sub)=="list"){
           newKey[[1+length(newKey)]]<-"value_col"
-        }  
-        dataKeys[[1+length(dataKeys)]]<-newKey 
+        }
+        dataKeys[[1+length(dataKeys)]]<-newKey
       }
     }
   }
-  
+
   settings_values <- map(dataKeys, function(x) {return(getSettingValue(x, settings))})
 
   common_cols <- intersect(col_names,settings_values)
@@ -51,10 +51,10 @@ trimData <- function(data, settings, chart="edish"){
 
   ## Remove rows if baseline or analysisFlag is specified ##
   baselineSetting<-settings[['baseline']][['value_col']]
-  baselineMissing <- is.null(baselineSetting) || is.na(baselineSetting)
+  baselineMissing <- is.null(baselineSetting)
   analysisSetting<-settings[['analysisFlag']][['value_col']]
-  analysisMissing <- is.null(analysisSetting) || is.na(analysisSetting)
-  
+  analysisMissing <- is.null(analysisSetting)
+
   if(!baselineMissing | !analysisMissing) {
 
     # Create Baseline String

tests/testthat/test_generateSettings.R

@@ -28,13 +28,13 @@ test_that("data mappings are null when setting=none, character otherwise",{
   none_settings <- generateSettings(standard="None")
   for(text_key in data_setting_keys){
     key<-textKeysToList(text_key)[[1]]
-    expect_equal(getSettingValue(settings=none_settings,key=key),NA)
+    expect_equal(getSettingValue(settings=none_settings,key=key),NULL)
   }
 
   other_settings <- generateSettings(standard="a different standard") 
   for(text_key in data_setting_keys){
     key<-textKeysToList(text_key)[[1]]
-    expect_equal(getSettingValue(settings=other_settings,key=key),NA)
+    expect_equal(getSettingValue(settings=other_settings,key=key),NULL)
   }
 
   sdtm_settings <- generateSettings(standard="SDTM")
@@ -71,7 +71,7 @@ test_that("data mappings are null when setting=none, character otherwise",{
     if (text_key %in% c("id_col","measure_col","measure_values--ALT")) {
       expect_is(getSettingValue(settings=partial_adam_settings,key=key),"character")
     } else {
-      expect_equal(getSettingValue(settings=partial_adam_settings,key=key),NA)
+      expect_equal(getSettingValue(settings=partial_adam_settings,key=key),NULL)
     }
   }
 
@@ -92,7 +92,7 @@ test_that("data mappings are null when setting=none, character otherwise",{
   #non data mappings are NA
   for(text_key in option_keys){
     key<-textKeysToList(text_key)[[1]]
-    expect_equal(getSettingValue(settings=noDefaults,key=key),NA)
+    expect_equal(getSettingValue(settings=noDefaults,key=key),NULL)
   }
 
   #data mappings are filled as expected 

tests/testthat/test_generateShell.R

@@ -5,8 +5,8 @@ default <- generateShell()
 
 test_that("a list with the expected properties and structure is returned by default",{
   expect_type(default, "list")
-  expect_equal(default[["id_col"]],NA)
-  expect_equal(default[["measure_values"]][["ALT"]],NA)
+  expect_equal(default[["id_col"]],NULL)
+  expect_equal(default[["measure_values"]][["ALT"]],NULL)
   expect_null(default[["not_a_setting"]])
 })