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Merged
merged 3 commits into from
Mar 12, 2025
Merged

Update tests #421

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290c1ed
Update tests
koenderks Mar 12, 2025
20c4803
Update test-mlclusteringkmeans.R
koenderks Mar 12, 2025
f643b68
try clara?
koenderks Mar 12, 2025
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlclassificationboosting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ options$noOfFolds <- 5
options$deviancePlot <- TRUE
options$outOfBagImprovementPlot <- TRUE
options$relativeInfluencePlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlclassificationknn.R
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Expand Up @@ -38,7 +38,7 @@ options$modelValid <- "validationManual"
options$noOfFolds <- 5
options$errorVsKPlot <- TRUE
options$weightsPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlclassificationlda.R
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Expand Up @@ -19,7 +19,7 @@ options$modelOptimization <- "manual"
options$modelValid <- "validationManual"
options$multicolTable <- TRUE
options$noOfFolds <- 5
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlclassificationrandomforest.R
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Expand Up @@ -39,7 +39,7 @@ options$noOfFolds <- 5
options$accuracyDecreasePlot <- TRUE
options$purityIncreasePlot <- TRUE
options$treesVsModelErrorPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlclusteringdensitybased.R
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Expand Up @@ -9,7 +9,7 @@ options$distance <- "normalDensities"
options[["kDistancePlot"]] <- TRUE
options$modelOptimization <- "manual"
options$tsneClusterPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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4 changes: 2 additions & 2 deletions tests/testthat/test-mlclusteringfuzzycmeans.R
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Expand Up @@ -2,7 +2,7 @@ context("Machine Learning Fuzzy C-Means Clustering")

# Test fixed model #############################################################
options <- initMlOptions("mlClusteringFuzzyCMeans")
options$predictors <- list("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors.types <- rep("scale", length(options$predictors))
options$modelOptimization <- "manual"
options$predictionsColumn <- ""
Expand All @@ -22,7 +22,7 @@ options$predictionsColumn <- ""
options$validationMeasures <- TRUE
options$modelOptimization <- "optimized"
options$tsneClusterPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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4 changes: 2 additions & 2 deletions tests/testthat/test-mlclusteringhierarchical.R
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Expand Up @@ -2,7 +2,7 @@ context("Machine Learning Hierarchical Clustering")

# Test fixed model #############################################################
options <- initMlOptions("mlClusteringHierarchical")
options$predictors <- list("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors.types <- rep("scale", length(options$predictors))
options$modelOptimization <- "manual"
options$predictionsColumn <- ""
Expand All @@ -23,7 +23,7 @@ options$validationMeasures <- TRUE
options$dendrogram <- TRUE
options$modelOptimization <- "optimized"
options$tsneClusterPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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9 changes: 5 additions & 4 deletions tests/testthat/test-mlclusteringkmeans.R
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Expand Up @@ -2,7 +2,7 @@ context("Machine Learning K-Means Clustering")

# Test fixed model #############################################################
options <- initMlOptions("mlClusteringKMeans")
options$predictors <- list("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors.types <- rep("scale", length(options$predictors))
options$modelOptimization <- "manual"
options$predictionsColumn <- ""
Expand All @@ -18,7 +18,7 @@ jaspTools::expect_equal_tables(table,

# Test optimized model #########################################################
options <- initMlOptions("mlClusteringKMeans")
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
Expand Down Expand Up @@ -104,7 +104,7 @@ test_that("t-SNE Cluster Plot matches", {
context("Machine Learning K-Medians Clustering")

options <- initMlOptions("mlClusteringKMeans")
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
Expand Down Expand Up @@ -186,7 +186,7 @@ test_that("Elbow Method Plot matches", {
context("Machine Learning K-Medoids Clustering")

options <- initMlOptions("mlClusteringKMeans")
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
Expand All @@ -198,6 +198,7 @@ options$validationMeasures <- TRUE
options$elbowMethodPlot <- TRUE
options$clusterMeanPlot <- TRUE
options$centers <- "medoids"
options$algorithm <- "clara"
options$setSeed <- TRUE
options$modelOptimization <- "optimized"
options$addPredictions <- FALSE
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4 changes: 2 additions & 2 deletions tests/testthat/test-mlclusteringmodelbased.R
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Expand Up @@ -2,7 +2,7 @@ context("Machine Learning K-Means Clustering")

# Test fixed model #############################################################
options <- initMlOptions("mlClusteringModelBased")
options$predictors <- list("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors.types <- rep("scale", length(options$predictors))
options$modelOptimization <- "manual"
options$predictionsColumn <- ""
Expand All @@ -17,7 +17,7 @@ jaspTools::expect_equal_tables(table,

# Test optimized model #########################################################
options <- initMlOptions("mlClusteringModelBased")
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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4 changes: 2 additions & 2 deletions tests/testthat/test-mlclusteringrandomforest.R
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Expand Up @@ -2,7 +2,7 @@ context("Machine Learning Random Forest Clustering")

# Test fixed model #############################################################
options <- initMlOptions("mlClusteringRandomForest")
options$predictors <- list("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
options$predictors.types <- rep("scale", length(options$predictors))
options$modelOptimization <- "manual"
options$predictionsColumn <- ""
Expand Down Expand Up @@ -35,7 +35,7 @@ options$validationMeasures <- TRUE
options$featureImportanceTable <- TRUE
options$modelOptimization <- "optimized"
options$tsneClusterPlot <- TRUE
options$predictors <- list("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
options$predictors <- c("Alcohol", "Malic", "Ash", "Alcalinity", "Magnesium", "Phenols",
"Flavanoids", "Nonflavanoids", "Proanthocyanins", "Color",
"Hue", "Dilution", "Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlregressionboosting.R
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Expand Up @@ -49,7 +49,7 @@ options$deviancePlot <- TRUE
options$outOfBagImprovementPlot <- TRUE
options$relativeInfluencePlot <- TRUE
options$predictedPerformancePlot <- TRUE
options$predictors <- list("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
options$predictors <- c("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
"Nonflavanoids", "Proanthocyanins", "Color", "Hue", "Dilution",
"Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlregressionknn.R
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Expand Up @@ -46,7 +46,7 @@ options$modelValid <- "validationManual"
options$noOfFolds <- 5
options$errorVsKPlot <- TRUE
options$predictedPerformancePlot <- TRUE
options$predictors <- list("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
options$predictors <- c("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
"Nonflavanoids", "Proanthocyanins", "Color", "Hue", "Dilution",
"Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlregressionlinear.R
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Expand Up @@ -9,7 +9,7 @@ options$saveModel <- FALSE
options$holdoutData <- "holdoutManual"
options$modelOptimization <- "manual"
options$predictedPerformancePlot <- TRUE
options$predictors <- list("Petal.Width", "Sepal.Length", "Sepal.Width", "Species")
options$predictors <- c("Petal.Width", "Sepal.Length", "Sepal.Width", "Species")
options$predictors.types <- c("scale", "scale", "scale", "nominal")
options$setSeed <- TRUE
options$target <- "Petal.Length"
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlregressionrandomforest.R
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Expand Up @@ -48,7 +48,7 @@ options$accuracyDecreasePlot <- TRUE
options$purityIncreasePlot <- TRUE
options$treesVsModelErrorPlot <- TRUE
options$predictedPerformancePlot <- TRUE
options$predictors <- list("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
options$predictors <- c("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
"Nonflavanoids", "Proanthocyanins", "Color", "Hue", "Dilution",
"Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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2 changes: 1 addition & 1 deletion tests/testthat/test-mlregressionregularized.R
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Expand Up @@ -35,7 +35,7 @@ options$modelOptimization <- "optMin"
options$modelValid <- "validationManual"
options$noOfFolds <- 5
options$predictedPerformancePlot <- TRUE
options$predictors <- list("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
options$predictors <- c("Malic", "Ash", "Alcalinity", "Magnesium", "Phenols", "Flavanoids",
"Nonflavanoids", "Proanthocyanins", "Color", "Hue", "Dilution",
"Proline")
options$predictors.types <- rep("scale", length(options$predictors))
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