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Fix test issue #119

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Jul 11, 2024
Merged

Fix test issue #119

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9 changes: 3 additions & 6 deletions R/networkanalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 4 additions & 0 deletions tests/testthat/test-bayesiannetworkanalysis.R
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Expand Up @@ -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"]])
Expand All @@ -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)
Expand All @@ -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$manualColorGroups <- list(list(color = "red", name = "Group 1"), list(color = "red", name = "Group 2"))
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5 changes: 5 additions & 0 deletions tests/testthat/test-networkanalysis.R
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Expand Up @@ -8,6 +8,7 @@ context("Network Analysis")
options <- jaspTools::analysisOptions("NetworkAnalysis")
options$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
Expand Down Expand Up @@ -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")

Expand Down Expand Up @@ -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", {
Expand All @@ -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
Expand All @@ -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"
Expand Down
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