From 950bcdd31e2767359adba682b86d06689d58ac9e Mon Sep 17 00:00:00 2001 From: sisyphus-jasp Date: Fri, 6 Mar 2026 04:11:45 +0100 Subject: [PATCH] [jaspMachineLearning] Fix confusion matrix in Classification Boosting to display all... --- R/mlClassificationBoosting.R | 11 +- .../data-split.new.svg | 44 ++ .../relative-influence-plot.new.svg | 81 ++ .../data-split.new.svg | 44 ++ .../decision-tree-plot.new.svg | 77 ++ .../mlclassificationknn/data-split.new.svg | 44 ++ .../mlclassificationlda/data-split.new.svg | 42 + ...near-discriminant-matrix-subplot-1.new.svg | 34 + ...near-discriminant-matrix-subplot-2.new.svg | 34 + ...near-discriminant-matrix-subplot-3.new.svg | 34 + ...near-discriminant-matrix-subplot-4.new.svg | 59 ++ ...near-discriminant-matrix-subplot-5.new.svg | 227 ++++++ ...near-discriminant-matrix-subplot-6.new.svg | 34 + ...near-discriminant-matrix-subplot-8.new.svg | 59 ++ .../data-split-1.new.svg | 42 + .../data-split-2.new.svg | 42 + .../data-split.new.svg | 42 + .../data-split.new.svg | 44 ++ .../mean-decrease-in-accuracy.new.svg | 77 ++ .../total-increase-in-node-purity.new.svg | 81 ++ .../mlclassificationsvm/data-split.new.svg | 44 ++ .../all-predictors.new.svg | 340 ++++++++ .../k-distance-plot.new.svg | 70 ++ .../all-predictors.new.svg | 287 +++++++ .../all-predictors.new.svg | 456 +++++++++++ .../dendogram.new.svg | 745 ++++++++++++++++++ .../all-predictors-2.new.svg | 395 ++++++++++ .../all-predictors-3.new.svg | 346 ++++++++ .../mlclusteringkmeans/all-predictors.new.svg | 344 ++++++++ .../all-predictors.new.svg | 234 ++++++ .../all-predictors.new.svg | 234 ++++++ .../mlregressionboosting/data-split.new.svg | 44 ++ .../relative-influence-plot.new.svg | 79 ++ .../data-split.new.svg | 44 ++ .../decision-tree-plot.new.svg | 162 ++++ .../_snaps/mlregressionknn/data-split.new.svg | 44 ++ .../mlregressionlinear/data-split.new.svg | 42 + .../data-split.new.svg | 44 ++ .../mean-decrease-in-accuracy.new.svg | 81 ++ .../total-increase-in-node-purity.new.svg | 73 ++ .../data-split.new.svg | 44 ++ .../_snaps/mlregressionsvm/data-split.new.svg | 44 ++ 42 files changed, 5345 insertions(+), 3 deletions(-) create mode 100644 tests/testthat/_snaps/mlclassificationboosting/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationboosting/relative-influence-plot.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationdecisiontree/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationdecisiontree/decision-tree-plot.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationknn/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-1.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-2.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-3.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-4.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-5.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-6.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlda/linear-discriminant-matrix-subplot-8.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-1.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-2.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationnaivebayes/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationrandomforest/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationrandomforest/mean-decrease-in-accuracy.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationrandomforest/total-increase-in-node-purity.new.svg create mode 100644 tests/testthat/_snaps/mlclassificationsvm/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringdensitybased/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringdensitybased/k-distance-plot.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringfuzzycmeans/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringhierarchical/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringhierarchical/dendogram.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringkmeans/all-predictors-2.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringkmeans/all-predictors-3.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringkmeans/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringmodelbased/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlclusteringrandomforest/all-predictors.new.svg create mode 100644 tests/testthat/_snaps/mlregressionboosting/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressionboosting/relative-influence-plot.new.svg create mode 100644 tests/testthat/_snaps/mlregressiondecisiontree/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressiondecisiontree/decision-tree-plot.new.svg create mode 100644 tests/testthat/_snaps/mlregressionknn/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressionlinear/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressionrandomforest/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressionrandomforest/mean-decrease-in-accuracy.new.svg create mode 100644 tests/testthat/_snaps/mlregressionrandomforest/total-increase-in-node-purity.new.svg create mode 100644 tests/testthat/_snaps/mlregressionregularized/data-split.new.svg create mode 100644 tests/testthat/_snaps/mlregressionsvm/data-split.new.svg diff --git a/R/mlClassificationBoosting.R b/R/mlClassificationBoosting.R index 8edcfa69..bfd8c984 100644 --- a/R/mlClassificationBoosting.R +++ b/R/mlClassificationBoosting.R @@ -147,27 +147,32 @@ mlClassificationBoosting <- function(jaspResults, dataset, options, ...) { dataProbs <- gbm::predict.gbm(fit, newdata = dataset, n.trees = noOfTrees, type = "response") dataPredictions <- colnames(dataProbs)[apply(dataProbs, 1, which.max)] testPredictions <- dataPredictions[-trainingIndex] + targetLevels <- levels(dataset[, options[["target"]]]) + testPredictions <- factor(testPredictions, levels = targetLevels) + testReal <- factor(testSet[, options[["target"]]], levels = targetLevels) # Create results object result <- list() result[["model"]] <- fit result[["formula"]] <- formula result[["noOfFolds"]] <- noOfFolds result[["noOfTrees"]] <- noOfTrees - result[["confTable"]] <- table("Pred" = testPredictions, "Real" = testSet[, options[["target"]]]) + result[["confTable"]] <- table("Pred" = testPredictions, "Real" = testReal) result[["testAcc"]] <- sum(diag(prop.table(result[["confTable"]]))) result[["relInf"]] <- summary(fit, plot = FALSE) result[["auc"]] <- .classificationCalcAUC(testSet, trainingSet, options, "boostingClassification", noOfFolds = noOfFolds, noOfTrees = noOfTrees) result[["ntrain"]] <- nrow(trainingSet) result[["ntest"]] <- nrow(testSet) result[["testPred"]] <- testPredictions - result[["testReal"]] <- testSet[, options[["target"]]] + result[["testReal"]] <- testReal result[["train"]] <- trainingSet result[["test"]] <- testSet result[["method"]] <- if (options[["modelValid"]] == "validationManual") "OOB" else "" result[["testIndicatorColumn"]] <- testIndicatorColumn result[["classes"]] <- dataPredictions if (options[["modelOptimization"]] != "manual") { - result[["validationConfTable"]] <- table("Pred" = validationPredictions, "Real" = validationSet[, options[["target"]]]) + validationPredictions <- factor(validationPredictions, levels = targetLevels) + validationReal <- factor(validationSet[, options[["target"]]], levels = targetLevels) + result[["validationConfTable"]] <- table("Pred" = validationPredictions, "Real" = validationReal) result[["validAcc"]] <- sum(diag(prop.table(result[["validationConfTable"]]))) result[["nvalid"]] <- nrow(validationSet) result[["valid"]] <- validationSet diff --git a/tests/testthat/_snaps/mlclassificationboosting/data-split.new.svg b/tests/testthat/_snaps/mlclassificationboosting/data-split.new.svg new file mode 100644 index 00000000..689c5b50 --- /dev/null +++ b/tests/testthat/_snaps/mlclassificationboosting/data-split.new.svg @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + +Train: 114 +Validation: 29 +Test: 35 +Total: 178 + + + + + +data-split + + diff --git a/tests/testthat/_snaps/mlclassificationboosting/relative-influence-plot.new.svg b/tests/testthat/_snaps/mlclassificationboosting/relative-influence-plot.new.svg new file mode 100644 index 00000000..1293ceb8 --- /dev/null +++ b/tests/testthat/_snaps/mlclassificationboosting/relative-influence-plot.new.svg @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Proanthocyanins +Alcalinity +Nonflavanoids +Ash +Magnesium +Malic +Phenols +Dilution +Hue +Alcohol +Flavanoids +Color +Proline + + + + + + + + + +0 +5 +10 +15 +20 +25 +30 +35 +Relative Influence +relative-influence-plot + + diff --git a/tests/testthat/_snaps/mlclassificationdecisiontree/data-split.new.svg b/tests/testthat/_snaps/mlclassificationdecisiontree/data-split.new.svg new file mode 100644 index 00000000..b254084a --- /dev/null +++ b/tests/testthat/_snaps/mlclassificationdecisiontree/data-split.new.svg @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + +Train: 96 +Validation: 24 +Test: 30 +Total: 150 + + + + + +data-split + + diff --git 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+ + + + + + + + + + + + + + + + + + + + + + +-8 +-6 +-4 +-2 +0 +2 +4 +6 +Density +linear-discriminant-matrix-subplot-8 + + diff --git a/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-1.new.svg b/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-1.new.svg new file mode 100644 index 00000000..3af22552 --- /dev/null +++ b/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-1.new.svg @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + +Train: 160 +Test: 40 +Total: 200 + + + + + +data-split-1 + + diff --git a/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-2.new.svg b/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-2.new.svg new file mode 100644 index 00000000..a1148ca2 --- /dev/null +++ b/tests/testthat/_snaps/mlclassificationlogisticmultinomial/data-split-2.new.svg @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + +Train: 120 +Test: 30 +Total: 150 + + + + + 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