Updating data ingest to support preloading data (#227)

* removing old data reading from binary classification, testing, and estimation analyses

* Updating the unit tests to work with the data preloading

Updating the reference table for six of the binary testing unit tests to fix the spurious failures introduced with #218

Author: kylelang

R/LSbinaryclassification.R

@@ -122,21 +122,19 @@ LSbinaryclassification <- function(jaspResults, dataset, options, state = NULL)
 .bcReadData <- function(jaspResults, dataset, options, ready) {
   if(options[["inputType"]] != "data" || !ready) return(NULL)
 
-  if(is.null(dataset)) {
-    dataset <- .readDataSetToEnd(columns = c(options[["marker"]], options[["labels"]]))
-    dataset <- dataset[complete.cases(dataset),]
-
-    labels <- dataset[[options[["labels"]]]]
-    levels <- levels(as.factor(labels))
-    if(length(levels) != 2)    .quitAnalysis(gettext("The 'Positive condition (binary)' variable must have two levels!"))
-    if(any(table(labels) < 1)) .quitAnalysis(gettext("Each condition needs at least one observation."))
-
-    dataset <- data.frame(
-      marker    = dataset[[options[["marker"]]]],
-      condition = labels == levels[2], # second level is "positive" condition
-      test      = dataset[[options[["marker"]]]] >= options[["threshold"]]
-    )
-  }
+  dataset <- dataset[c(options[["marker"]], options[["labels"]])]
+  dataset <- dataset[complete.cases(dataset), ]
+
+  labels <- dataset[[options[["labels"]]]]
+  levels <- levels(as.factor(labels))
+  if(length(levels) != 2)    .quitAnalysis(gettext("The 'Positive condition (binary)' variable must have two levels!"))
+  if(any(table(labels) < 1)) .quitAnalysis(gettext("Each condition needs at least one observation."))
+
+  dataset <- data.frame(
+    marker    = dataset[[options[["marker"]]]],
+    condition = labels == levels[2], # second level is "positive" condition
+    test      = dataset[[options[["marker"]]]] >= options[["threshold"]]
+  )
 
   if(mean(subset(dataset, condition)$marker) < mean(subset(dataset, !condition)$marker))
     .quitAnalysis(gettextf("Mean of marker in positive condition (%1$s) needs to be larger than the mean of marker in negative condition (%2$s).", levels[2], levels[1]))

R/LSbinomialcommon.R

@@ -57,12 +57,7 @@
 
       } else if (options[["dataInputType"]] == "variable") {
 
-        # this is stupidly written #rework
-        if (!is.null(dataset)) {
-          tempY <- dataset
-        } else {
-          tempY <- .readDataSetToEnd(columns = options[["dataVariableSelected"]])[,1]
-        }
+        tempY <- dataset[[ options[["dataVariableSelected"]] ]]
 
       }
 

R/LSgaussiancommon.R

@@ -50,13 +50,7 @@
 
     } else if (options[["dataInputType"]] == "variable") {
 
-      # this is stupidly written #rework
-      if (!is.null(dataset)) {
-        tempY <- dataset
-      } else{
-        tempY <- .readDataSetToEnd(columns = options[["dataVariableSelected"]])[,1]
-      }
-
+      tempY   <- dataset[[ options[["dataVariableSelected"]] ]]
       data$SD <- options[["dataVariableSd"]]
 
     }

inst/Description.qml

@@ -9,6 +9,7 @@ Description
 	description:	qsTr("Learn Bayesian statistics with simple examples and supporting text")
 	version			: "0.19.2"
 	requiresData:	false
+	preloadData:	true
 	author:			"JASP Team"
 	maintainer:		"JASP Team <info@jasp-stats.org>"
 	website:		"www.jasp-stats.org"