From 60e01a09b4576aa504d755be0f995d61e26befd9 Mon Sep 17 00:00:00 2001
From: Koen Derks <koen-derks@hotmail.com>
Date: Thu, 10 Oct 2024 15:34:48 +0200
Subject: [PATCH] Update auditCommonFunctions.R

---
 R/auditCommonFunctions.R | 25 ++++++++++++++++---------
 inst/Description.qml     |  2 +-
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/R/auditCommonFunctions.R b/R/auditCommonFunctions.R
index e2d3453c..5c07af94 100644
--- a/R/auditCommonFunctions.R
+++ b/R/auditCommonFunctions.R
@@ -286,22 +286,29 @@
 #####################################
 
 .jfaExecutionStage <- function(options, jaspResults) {
-  if (options[["pasteVariables"]]) {
-    # Add the two computed colums to the data set
-    planningOptions <- .jfaInputOptionsGather(options, dataset = NULL, jaspResults, stage = "planning", rawData = TRUE)
+  if (is.null(jaspResults[["indicator_col"]])) {
+    jaspResults[["indicator_col"]] <- createJaspColumn(columnName = options[["indicator_col"]], dependencies = "indicator_col")
+  }
+  if (options[["executionChecked"]]) {
     selectionState <- .jfaSelectionState(options, dataset, jaspResults[["planningState"]], jaspResults[["selectionContainer"]])
-
     sample <- selectionState[["sample"]]
     dataset <- .readDataSetToEnd(columns.as.numeric = options[["id"]])
     sampleFilter <- numeric(selectionState[["N.items"]])
     rowNumber <- as.numeric(sample[["row"]])
     sampleFilter[rowNumber] <- as.numeric(sample[["times"]])
-    
-    if (is.null(jaspResults[["indicator_col"]])) {
-      jaspResults[["indicator_col"]] <- createJaspColumn(columnName = options[["indicator_col"]], dependencies = "indicator_col")
-    }
-
     jaspResults[["indicator_col"]]$setOrdinal(sampleFilter)
+    if (options[["annotation"]] == "binary") { # Overwrite the empty column with 0's
+      auditDataVariable <- rep(NA, selectionState[["N.items"]])
+      if (is.null(jaspResults[["variable_col"]])) {
+        auditDataVariable[rowNumber] <- 0
+      } else {
+        auditDataVariable[options[["performAudit"]][[1]]$rowIndices] <- base::pmin(options[["performAudit"]][[1]]$values, 1)
+      }
+      if (options[["pasteVariables"]]) {
+        jaspResults[["variable_col"]] <- createJaspColumn(columnName = options[["variable_col"]], dependencies = "variable_col")
+        jaspResults[["variable_col"]]$setScale(auditDataVariable)
+      }
+    }
   }
 }
 
diff --git a/inst/Description.qml b/inst/Description.qml
index 22dd5327..fbcc6204 100644
--- a/inst/Description.qml
+++ b/inst/Description.qml
@@ -10,7 +10,7 @@ Description
 	author				: "Koen Derks, Jacques de Swart, Eric-Jan Wagenmakers, Jan Wille and Ruud Wetzels"
 	maintainer			: "Koen Derks <k.derks@nyenrode.nl>"
 	website				: "www.github.com/koenderks/jfa"
-	preloadData        : false
+	preloadData			: false
 	license				: "GPL (>= 3)"
 	icon				: "audit-module.svg"