Add intercept option

Author: koenderks

R/commonMachineLearningClassification.R

@@ -32,7 +32,8 @@
     "mutationMethod", "survivalMethod", "elitismProportion", "candidates",                # Neural network
     "noOfTrees", "maxTrees", "baggingFraction", "noOfPredictors", "numberOfPredictors",   # Random forest
     "complexityParameter", "degree", "gamma", "cost", "tolerance", "epsilon", "maxCost",  # Support vector machine
-    "smoothingParameter"                                                                  # Naive Bayes
+    "smoothingParameter",                                                                 # Naive Bayes
+    "intercept"                                                                           # Logistic
   )
   if (includeSaveOptions) {
     opt <- c(opt, "saveModel", "savePath")

R/mlClassificationLogistic.R

@@ -78,6 +78,12 @@ mlClassificationLogistic <- function(jaspResults, dataset, options, ...) {
   testIndicatorColumn[trainingIndex] <- 0
   # Just create a train and a test set (no optimization)
   testSet <- dataset[-trainingIndex, ]
+  # Create the formula
+  if (options[["intercept"]]) {
+    formula <- formula(paste(options[["target"]], "~ 1 + ", paste(options[["predictors"]], collapse = " + ")))
+  } else {
+    formula <- formula(paste(options[["target"]], "~ 0 + ", paste(options[["predictors"]], collapse = " + ")))
+  }
   if (nlevels(trainingSet[[options[["target"]]]]) == 2) {
     family = "binomial"
     trainingFit <- stats::glm(formula, data = trainingSet, family = family)

inst/qml/mlClassificationLogistic.qml

@@ -24,6 +24,7 @@ import JASP.Widgets		1.0
 import "./common/ui" as UI
 import "./common/tables" as TAB
 import "./common/figures" as FIG
+import "./common/analyses/regularized" as REGU
 
 Form
 {
@@ -63,6 +64,7 @@ Form
 		{
 			title: qsTr("Algorithmic Settings")
 
+			REGU.Intercept { }
 			UI.ScaleVariables { }
 			UI.SetSeed { }
 		}

tests/testthat/helper-ml.R

@@ -27,7 +27,7 @@ mlOptions <- function(analysis) {
     files <- c(files, list.files(testthat::test_path("..", "..", "inst", "qml", "common", "analyses", "randomforest"), full.names = TRUE))
   } else if (analysis %in% c("mlClassificationSvm", "mlRegressionSvm")) {
     files <- c(files, list.files(testthat::test_path("..", "..", "inst", "qml", "common", "analyses", "svm"), full.names = TRUE))
-  } else if (analysis %in% c("mlRegressionLinear", "mlRegressionRegularized")) {
+  } else if (analysis %in% c("mlClassificationLogistic", "mlRegressionLinear", "mlRegressionRegularized")) {
     files <- c(files, list.files(testthat::test_path("..", "..", "inst", "qml", "common", "analyses", "regularized"), full.names = TRUE))
   }
   options <- lapply(files, jaspTools:::readQML) |>