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Remove readDataSetToEnd #108

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Remove readDataSetToEnd #108

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8436178
Remove readDataSetToEnd
maltelueken Oct 10, 2024
ddde3ad
Rename 'debug' to 'debug.csv' in all tests
maltelueken Oct 10, 2024
5f10176
Fix unit test for .procReplaceDummyVars
maltelueken Oct 10, 2024
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2 changes: 0 additions & 2 deletions R/bayesianProcess.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,6 @@ BayesianProcess <- function(jaspResults, dataset = NULL, options) {
return()
}
options$naAction <- "listwise"
# Read dataset
dataset <- .procReadData(options)
# Check for errors in dataset
.procErrorHandling(dataset, options)
# Create a container for each model
Expand Down
4 changes: 1 addition & 3 deletions R/classicProcess.R
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,6 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
.procModelSummaryTable(jaspResults, options, NULL)
return()
}
# Read dataset
dataset <- .procReadData(options)
# Check for errors in dataset
.procErrorHandling(dataset, options)
# Create a container for each model
Expand Down Expand Up @@ -468,7 +466,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
return(graph)
}

.procReadData <- function(options) {
.procReadData <- function(dataset, options) {
# Read in selected variables from dataset
dataset <- .readDataSetToEnd(
columns.as.numeric = c(options[['dependent']], options[['covariates']]),
Expand Down
1 change: 1 addition & 0 deletions inst/Description.qml
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Expand Up @@ -12,6 +12,7 @@ Description
maintainer : "JASP Team <[email protected]>"
website : "https://jasp-stats.org"
license : "GPL (>= 2)"
preloadData : true

GroupTitle
{
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-bayesian-process-general.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ test_that("Missing values work without independent covariances", {
options$processModels[[1]]$independentCovariances <- FALSE
options$processModels[[1]]$intercepts <- TRUE
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)

table <- results[["results"]][["modelSummaryTable"]][["data"]]
jaspTools::expect_equal_tables(table,
Expand Down Expand Up @@ -90,7 +90,7 @@ test_that("Incomplete Hayes configuration works", {
options$processModels[[1]]$modelNumber <- 5
options$processModels[[1]]$localTests <- TRUE
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)

plotName <- results[["results"]][["pathPlotContainer"]][["collection"]][["pathPlotContainer_Model 1"]][["collection"]][["pathPlotContainer_Model 1_conceptPathPlot"]][["data"]]
testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
Expand Down
32 changes: 16 additions & 16 deletions tests/testthat/test-bayesian-process-integration.R
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -168,7 +168,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "facExperim")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -293,7 +293,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -481,7 +481,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -657,7 +657,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -885,7 +885,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -1103,7 +1103,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "mediators", processVariable = "debCollin1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -1215,7 +1215,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "mediators", processVariable = "debCollin1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -1334,7 +1334,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -1602,7 +1602,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -1840,7 +1840,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -2124,7 +2124,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor2")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -2382,7 +2382,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "mediators", processVariable = "contcor1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -2558,7 +2558,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "mediators", processVariable = "contcor1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -2741,7 +2741,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "contcor1")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down Expand Up @@ -2987,7 +2987,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
processType = "moderators", processVariable = "facExperim")),
residualCovariances = TRUE, statisticalPathPlot = TRUE, totalEffects = TRUE))
set.seed(1)
results <- jaspTools::runAnalysis("BayesianProcess", "debug", options)
results <- jaspTools::runAnalysis("BayesianProcess", "debug.csv", options)



Expand Down
36 changes: 18 additions & 18 deletions tests/testthat/test-classic-process-integration-custom-models.R
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -142,7 +142,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -251,7 +251,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -343,7 +343,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -437,7 +437,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -566,7 +566,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -698,7 +698,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -817,7 +817,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -937,7 +937,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1057,7 +1057,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1179,7 +1179,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1308,7 +1308,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1437,7 +1437,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1584,7 +1584,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1723,7 +1723,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1852,7 +1852,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -1985,7 +1985,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down Expand Up @@ -2119,7 +2119,7 @@ options$processModels <- list(list(conceptualPathPlot = TRUE, independentCovaria
localTests = FALSE, localTestType = "cis", localTestBootstrap = FALSE,
localTestBootstrapSamples = 1000))
set.seed(1)
results <- jaspTools::runAnalysis("ClassicProcess", "debug", options)
results <- jaspTools::runAnalysis("ClassicProcess", "debug.csv", options)



Expand Down
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