From 4a1c6778887b13fbc106e696412bc5855b823aa6 Mon Sep 17 00:00:00 2001
From: Don van den Bergh <donvdbergh@hotmail.com>
Date: Tue, 18 Jun 2024 13:57:34 +0200
Subject: [PATCH] changes for new variablesList/ data reading

---
 R/networkanalysis.R                  | 11 ++++++----
 inst/qml/BayesianNetworkAnalysis.qml | 32 ++++++++++++++--------------
 inst/qml/NetworkAnalysis.qml         |  4 ++--
 3 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/R/networkanalysis.R b/R/networkanalysis.R
index 5dd5181..46f85fa 100644
--- a/R/networkanalysis.R
+++ b/R/networkanalysis.R
@@ -56,10 +56,13 @@ NetworkAnalysis <- function(jaspResults, dataset, options) {
   groupingVariable <- options[["groupingVariable"]]
   vars2read <- c(variables, groupingVariable)
   vars2read <- vars2read[vars2read != ""]
-  exclude    <- c()
-  if (options[["missingValues"]] == "listwise")
-    exclude <- vars2read
-  dataset <- .readDataSetToEnd(columns.as.numeric = vars2read, exclude.na.listwise = exclude)
+
+  exclude <- if (options[["missingValues"]] == "listwise")
+    c(vars2read, groupingVariable)
+  else if (groupingVariable != "")
+    exclude <- groupingVariable
+
+  dataset <- .readDataSetToEnd(columns.as.numeric = variables, columns.as.factor = if (groupingVariable != "") groupingVariable else NULL, exclude.na.listwise = exclude)
   # dataset <- .readDataSetToEnd(columns = vars2read, exclude.na.listwise = exclude) # jaspTools need this, JASP the line above
 
   if (options[["groupingVariable"]] == "") { # one network
diff --git a/inst/qml/BayesianNetworkAnalysis.qml b/inst/qml/BayesianNetworkAnalysis.qml
index 9f2cb9e..b3d8efb 100644
--- a/inst/qml/BayesianNetworkAnalysis.qml
+++ b/inst/qml/BayesianNetworkAnalysis.qml
@@ -27,10 +27,10 @@ Form
 	VariablesForm
 	{
 		AvailableVariablesList { name: "allVariablesList" }
-		AssignedVariablesList { name: "variables";			title: qsTr("Dependent Variables"); suggestedColumns: ["scale"]; id: networkVariables}
-		AssignedVariablesList { name: "groupingVariable";	title: qsTr("Split"); singleVariable: true; suggestedColumns: ["ordinal", "nominal"] }
+		AssignedVariablesList { name: "variables";			title: qsTr("Dependent Variables"); allowedColumns: ["scale"]; minNumericLevels: 2; id: networkVariables}
+		AssignedVariablesList { name: "groupingVariable";	title: qsTr("Split"); singleVariable: true; allowedColumns: ["nominal"]; minLevels: 2 }
 	}
-	
+
 	DropDown
 	{
 		id: estimator
@@ -47,8 +47,8 @@ Form
 	{
 		title: qsTr("Plots")
 		CheckBox { name: "networkPlot";		label: qsTr("Network plot")								}
-		CheckBox { 
-		  name: "evidencePlot";		
+		CheckBox {
+		  name: "evidencePlot";
 		  label: qsTr("Edge evidence plot")
 		  IntegerField {
 				  name:         "edgeInclusionCriteria";
@@ -61,12 +61,12 @@ Form
 				  CheckBox { name: "edgeExclusion";  label: qsTr("Evidence for exclusion"); checked: true }
 				  CheckBox { name: "edgeAbsence"; label: qsTr("Absence of evidence");   checked: true }
 		}
-		CheckBox { 
-		  name: "centralityPlot";  label: qsTr("Centrality plot") 
-		  CheckBox { 
+		CheckBox {
+		  name: "centralityPlot";  label: qsTr("Centrality plot")
+		  CheckBox {
 				    name:    "credibilityInterval";
 				    label:   qsTr("Credibility interval 95%");
-				    checked: false 
+				    checked: false
 		  }
 	  }
 	}
@@ -75,7 +75,7 @@ Form
 	{
 		title: qsTr("Tables")
 		CheckBox { name: "weightsMatrixTable";	label: qsTr("Weights matrix")	}
-		CheckBox { 
+		CheckBox {
 		    name: "edgeEvidenceTable";		label: qsTr("Edge evidence probability table")
 		    RadioButtonGroup {
 				  name: "evidenceType";
@@ -87,14 +87,14 @@ Form
 		}
 		CheckBox { name: "centralityTable"; label: qsTr("Centrality table") }
 	}
-	
-	Section 
+
+	Section
 	{
 	  title: qsTr("Sampling Options")
 	  Layout.columnSpan: 2
 	  IntegerField { name: "burnin"; label: qsTr("Burn in: "); value: "5000" ; min: 0; max: iter.value / 2; fieldWidth: 100; id: burnin }
 	  IntegerField { name: "iter"; label: qsTr("Iterations: "); value: "10000" ; min: burnin.value * 2; fieldWidth: 100; id: iter }
-		
+
 		SetSeed{}
 	}
 
@@ -103,7 +103,7 @@ Form
 		title: qsTr("Prior")
 
 		FormulaField { name: "gprior"; label: qsTr("Prior edge inclusion (g prior): "); value: "0.5" ; min: 0.001; max: 1; Layout.columnSpan: 2 }
-		
+
 		DropDown
 	  {
 		  id: initialConfiguration
@@ -245,7 +245,7 @@ Form
 			RadioButton { value: "inNodes";			label: qsTr("In plot");	 checked: true	}
 			RadioButton { value: "inLegend";		label: qsTr("In legend")					}
 		}
-		
+
 		RadioButtonGroup
 		{
 			name: "legend"
@@ -291,7 +291,7 @@ Form
 			CheckBox	{	name: "expectedInfluence";	label: qsTr("Expected influence");	checked: true	}
 		}
 	}
-	
+
 	Section
 	{
 		title:		qsTr("Network structure selection")
diff --git a/inst/qml/NetworkAnalysis.qml b/inst/qml/NetworkAnalysis.qml
index d1bc7b4..6a205f4 100644
--- a/inst/qml/NetworkAnalysis.qml
+++ b/inst/qml/NetworkAnalysis.qml
@@ -27,8 +27,8 @@ Form
 	VariablesForm
 	{
 		AvailableVariablesList { name: "allVariablesList" }
-		AssignedVariablesList { name: "variables";			title: qsTr("Dependent Variables"); suggestedColumns: ["ordinal", "scale"]; id: networkVariables}
-		AssignedVariablesList { name: "groupingVariable";	title: qsTr("Split"); singleVariable: true; suggestedColumns: ["ordinal", "nominal"] }
+		AssignedVariablesList { name: "variables";			title: qsTr("Dependent Variables");			allowedColumns: ["scale"]; minNumericLevels: 2; id: networkVariables}
+		AssignedVariablesList { name: "groupingVariable";	title: qsTr("Split"); singleVariable: true; allowedColumns: ["nominal"]; minLevels: 2 }
 	}
 
 	DropDown