fix data reading and unit tests

R/networkanalysis.R

@@ -52,15 +52,12 @@ NetworkAnalysis <- function(jaspResults, dataset, options) {
   if (!is.null(dataset))
     return(dataset)
 
-  variables <- unlist(options[["variables"]])
-  groupingVariable <- options[["groupingVariable"]]
-  vars2read <- c(variables, groupingVariable)
-  vars2read <- vars2read[vars2read != ""]
+  vars2read <- c("variables", "groupingVariable")
   exclude    <- c()
   if (options[["missingValues"]] == "listwise")
     exclude <- vars2read
-  dataset <- .readDataSetToEnd(columns.as.numeric = vars2read, exclude.na.listwise = exclude)
-  # dataset <- .readDataSetToEnd(columns = vars2read, exclude.na.listwise = exclude) # jaspTools need this, JASP the line above
+
+  dataset <- jaspBase::readDataSetByVariableTypes(options, vars2read, exclude.na.listwise = exclude)
 
   if (options[["groupingVariable"]] == "") { # one network
     dataset <- list(dataset) # for compatability with the split behaviour

tests/testthat/test-bayesiannetworkanalysis.R

@@ -11,6 +11,7 @@ testthat::test_that("Analysis handles too many missing values errors", {
   options <- jaspTools::analysisOptions("BayesianNetworkAnalysis")
   options$estimator <- "gcgm"
   options$variables <- c("contNormal", "contGamma", "debMiss99")
+  options$variables.types <- rep("scale", length(options$variables))
   results <- jaspTools::runAnalysis("BayesianNetworkAnalysis", "test.csv", options)
 
   testthat::expect_true(results[["results"]][["error"]])
@@ -21,7 +22,9 @@ testthat::test_that("Analysis handles too many missing values errors with groupi
   options <- jaspTools::analysisOptions("BayesianNetworkAnalysis")
   options$estimator <- "gcgm"
   options$variables <- c("contNormal", "contGamma", "debMiss80")
+  options$variables.types <- rep("scale", length(options$variables))
   options$groupingVariable <- "facFifty"
+  options$groupingVariable.types <- "nominal"
   options$dfprior <- 3
   options$gprior  <- "0.5"
   results <- jaspTools::runAnalysis("BayesianNetworkAnalysis", "test.csv", options)
@@ -46,6 +49,7 @@ testthat::test_that("Centrality plot works with empty graphs", {
   options <- analysisOptions("BayesianNetworkAnalysis")
   options$estimator <- "gcgm"
   options$variables <- c("extra", "group", "ID")
+  options$variables.types <- rep("scale", length(options$variables))
   options$dfprior <- 3
   options$gprior  <- "0.5"
   options$manualColorGroups <- list(list(color = "red", name = "Group 1"), list(color = "red", name = "Group 2"))

tests/testthat/test-networkanalysis.R

@@ -8,6 +8,7 @@ context("Network Analysis")
 options <- jaspTools::analysisOptions("NetworkAnalysis")
 options$estimator <- "ebicGlasso"
 options$variables <- c("contNormal", "contcor1", "contcor2")
+options$variables.types <- rep("scale", length(options$variables))
 options$centralityTable <- TRUE
 options$clusteringTable <- TRUE
 options$weightsMatrixTable <- TRUE
@@ -60,6 +61,7 @@ options$centralityTable <- TRUE
 options$clusteringTable <- TRUE
 options$weightsMatrixTable <- TRUE
 options$variables <- list("A1", "A2", "A3", "A4", "A5")
+options$variables.types <- rep("scale", length(options$variables))
 estimators <- c("ebicGlasso","cor","pcor","isingFit","isingSampler","huge","adalasso")
 file <- testthat::test_path("networkResults.rds")
 
@@ -177,6 +179,7 @@ dataset <- as.data.frame(dataset)
 options <- jaspTools::analysisOptions("NetworkAnalysis")
 options$estimator <- "ebicGlasso"
 options$variables <- c("V1", "V2", "V3")
+options$variables.types <- rep("scale", length(options$variables))
 results <- jaspTools::runAnalysis("NetworkAnalysis", dataset, options)
 
 test_that("Too many missing rows returns an error", {
@@ -198,6 +201,7 @@ dataset$layoutY <- c("V1 = 1", "V2 = 0")
 options <- jaspTools::analysisOptions("NetworkAnalysis")
 options$estimator <- "ebicGlasso"
 options$variables <- c("V1", "V2", "V3")
+options$variables.types <- rep("scale", length(options$variables))
 options$layoutX <- "layoutX"
 options$layoutY <- "layoutY"
 options$networkPlot <- TRUE
@@ -215,6 +219,7 @@ test_that("Incorrect user layout shows a warning", {
 options <- analysisOptions("NetworkAnalysis")
 options$estimator <- "pcor"
 options$variables <- c(paste0("A", 1:5), paste0("O", 1:5), paste0("E", 1:5))
+options$variables.types <- rep("ordinal", length(options$variables))
 options$networkPlot <- TRUE
 options$weightsMatrixTable <- TRUE
 options$thresholdBox <- "method"