From 4d4d8b90daf76aaf54e93fbb5ab22826611692e1 Mon Sep 17 00:00:00 2001
From: Don van den Bergh <donvdbergh@hotmail.com>
Date: Tue, 8 Oct 2024 16:59:15 +0200
Subject: [PATCH] fixes for new data reading (#122)

* fixes for new data reading

* cleanup Description.qml (spaces -> tabs)
---
 R/networkanalysis.R                   | 30 +++++++++++++++--------
 inst/Description.qml                  | 34 +++++++++++++--------------
 tests/testthat/test-networkanalysis.R |  4 ++--
 3 files changed, 39 insertions(+), 29 deletions(-)

diff --git a/R/networkanalysis.R b/R/networkanalysis.R
index 69377b9..a95e56a 100644
--- a/R/networkanalysis.R
+++ b/R/networkanalysis.R
@@ -49,15 +49,20 @@ NetworkAnalysis <- function(jaspResults, dataset, options) {
 
 .networkAnalysisReadData <- function(dataset, options) {
 
-  if (!is.null(dataset))
-    return(dataset)
-
-  vars2read <- c("variables", "groupingVariable")
-  exclude    <- c()
-  if (options[["missingValues"]] == "listwise")
-    exclude <- vars2read
+  layoutVariables <- c(options[["layoutX"]], options[["layoutY"]])
+  layoutVariables <- layoutVariables[layoutVariables != ""]
+  hasLayoutData <- length(layoutVariables) > 0L
+  if (hasLayoutData) {
+    layoutData <- dataset[layoutVariables]
+    layoutData <- jaspBase::excludeNaListwise(layoutData, layoutVariables)
+    # remove the two layout columns
+    dataset[layoutVariables] <- list(NULL)
+  }
 
-  dataset <- jaspBase::readDataSetByVariableTypes(options, vars2read, exclude.na.listwise = exclude)
+  if (options[["missingValues"]] == "listwise") {
+    exclude <- c(options[["variables"]], options[["groupingVariable"]])
+    dataset <- jaspBase::excludeNaListwise(dataset, exclude[exclude != ""])
+  }
 
   if (options[["groupingVariable"]] == "") { # one network
     dataset <- list(dataset) # for compatability with the split behaviour
@@ -68,6 +73,10 @@ NetworkAnalysis <- function(jaspResults, dataset, options) {
     dataset <- split(dataset, groupingVariableData, drop = TRUE)
     attr(dataset, "groupingVariableData") <- groupingVariableData
   }
+
+  if (hasLayoutData)
+    attr(dataset, "layoutData") <- layoutData
+
   return(dataset)
 
 }
@@ -1289,8 +1298,9 @@ NetworkAnalysis <- function(jaspResults, dataset, options) {
   # it turns out that we must save the layout in the A1 = ... style.
   if (options[["layoutX"]] != "" && options[["layoutY"]] != "") {
 
-    layoutXData <- .readDataSetToEnd(columns = options[["layoutX"]], exclude.na.listwise = options[["layoutX"]])[[1L]]
-    layoutYData <- .readDataSetToEnd(columns = options[["layoutY"]], exclude.na.listwise = options[["layoutY"]])[[1L]]
+    layoutData <- attr(dataset, "layoutData")
+    layoutXData <- layoutData[[1L]]
+    layoutYData <- layoutData[[2L]]
     variables <- unlist(options[["variables"]])
     layoutInfo <- .networkAnalysisSanitizeLayoutData(variables, layoutXData, layoutYData, options[["layoutX"]], options[["layoutY"]])
 
diff --git a/inst/Description.qml b/inst/Description.qml
index ea29bc2..1176399 100644
--- a/inst/Description.qml
+++ b/inst/Description.qml
@@ -12,33 +12,33 @@ Description
 	maintainer:		"JASP Team <info@jasp-stats.org>"
 	website:		"jasp-stats.org"
 	license:		"GPL (>= 2)"
+	preloadData:	true
 
+	GroupTitle
+	{
+		title:	"Classical"
+		icon:	"analysis-network.svg"
+	}
 
-  GroupTitle
-  {
-  	title:	"Classical"
-  	icon:			"analysis-network.svg"
-  }
-  
 	Analysis
 	{
 		title:	qsTr("Network Analysis")
-		qml:    "NetworkAnalysis.qml"
-		func:	  "NetworkAnalysis"
+		qml:	"NetworkAnalysis.qml"
+		func:	"NetworkAnalysis"
 	}
-	
+
 	Separator {}
-	
+
 	GroupTitle
-  {
-  	title:	"Bayesian"
-  	icon:		"bayesian-analysis-network.svg"
-  }
-	
+	{
+		title:	"Bayesian"
+		icon:		"bayesian-analysis-network.svg"
+	}
+
 	Analysis
 	{
 		title:	qsTr("Bayesian Network Analysis")
-		qml:    "BayesianNetworkAnalysis.qml"
-		func:	  "BayesianNetworkAnalysis"
+		qml:	"BayesianNetworkAnalysis.qml"
+		func:	"BayesianNetworkAnalysis"
 	}
 }
diff --git a/tests/testthat/test-networkanalysis.R b/tests/testthat/test-networkanalysis.R
index 7078915..63e013b 100644
--- a/tests/testthat/test-networkanalysis.R
+++ b/tests/testthat/test-networkanalysis.R
@@ -196,8 +196,8 @@ n <- 50
 p <- 3
 dataset <- as.data.frame(matrix(rnorm(n * (p-1)), n, p-1))
 dataset$V3 <- dataset$V1 + dataset$V2 + rnorm(n)
-dataset$layoutX <- c("V1 = 1", "V2 = 0")
-dataset$layoutY <- c("V1 = 1", "V2 = 0")
+dataset$layoutX <- factor(c("V1 = 1", "V2 = 0"))
+dataset$layoutY <- factor(c("V1 = 1", "V2 = 0"))
 options <- jaspTools::analysisOptions("NetworkAnalysis")
 options$estimator <- "ebicGlasso"
 options$variables <- c("V1", "V2", "V3")