Updates parameters in .project file + added test mandatory feature an…

…d BA constraint
mi-erasmusmc · Sep 3, 2024 · 4969782 · 4969782
1 parent fae9e6e
commit 4969782
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Showing 15 changed files with 111 additions and 47 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     pracma
 Encoding: UTF-8
 LinkingTo: Rcpp, BH (>= 1.51.0), RcppParallel
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     testthat (>= 3.0.0),
     knitr,

diff --git a/inst/examples/complexity/binary_10.project b/inst/examples/complexity/binary_10.project
@@ -8,7 +8,7 @@ IncrementalOutputFile=false
 [Setup]
 PartitionMethod=RESUBSTITUTION
 Randomize=no
-StartRulelength=3
+StartRulelength=1
 EndRulelength=3
 LearnRatio=0.8
 NumberofPartitions=1
@@ -34,17 +34,16 @@ PrintCutoffMethod=no
 PrintCutoffValues=no
 PrintOperatorMethod=no
 PrintOperatorValues=no
-PrintCombinations=yes
-PrintFeatureSets=yes
+PrintCombinations=no
+PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=no
 Parallel=no
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
 
diff --git a/inst/examples/complexity/binary_3.project b/inst/examples/complexity/binary_3.project
@@ -34,17 +34,16 @@ PrintCutoffMethod=no
 PrintCutoffValues=no
 PrintOperatorMethod=no
 PrintOperatorValues=no
-PrintCombinations=yes
-PrintFeatureSets=yes
+PrintCombinations=no
+PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=no
 Parallel=no
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
 
diff --git a/inst/examples/complexity/categorical_4.project b/inst/examples/complexity/categorical_4.project
@@ -34,17 +34,16 @@ PrintCutoffMethod=no
 PrintCutoffValues=no
 PrintOperatorMethod=no
 PrintOperatorValues=no
-PrintCombinations=yes
-PrintFeatureSets=yes
-PrintCutoffSets=yes
-PrintCutOffsetsBestLength=no
+PrintCombinations=no
+PrintFeatureSets=no
+PrintCutoffSets=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=no
 Parallel=no
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
 
diff --git a/inst/examples/complexity/continuous_4.project b/inst/examples/complexity/continuous_4.project
@@ -34,17 +34,16 @@ PrintCutoffMethod=no
 PrintCutoffValues=no
 PrintOperatorMethod=no
 PrintOperatorValues=no
-PrintCombinations=yes
-PrintFeatureSets=yes
-PrintCutoffSets=yes
-PrintCutOffsetsBestLength=no
+PrintCombinations=no
+PrintFeatureSets=no
+PrintCutoffSets=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=no
 Parallel=no
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
 
diff --git a/inst/examples/complexity/mix_4.project b/inst/examples/complexity/mix_4.project
@@ -25,26 +25,27 @@ FeatureRule=
 Maximize=BALANCEDACCURACY
 Accuracy=
 Specificity=
+BalancedAccuracy=0.6268
 [Output]
-OutputMethod=BEST
+OutputMethod=EVERY
 PrintSettings=yes
 PrintPartitions=no
 PrintFeatureOperators=no
 PrintCutoffMethod=no
 PrintCutoffValues=no
 PrintOperatorMethod=no
 PrintOperatorValues=no
-PrintCombinations=yes
-PrintFeatureSets=yes
+PrintCombinations=no
+PrintFeatureSets=no
 PrintCutoffSets=no
 PrintCutOffsetsBestLength=no
-PrintPerformance=yes
+PrintPerformance=no
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=no
 Parallel=no
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
 
diff --git a/inst/examples/plp/test_plp.project b/inst/examples/plp/test_plp.project
@@ -38,7 +38,6 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no

diff --git a/inst/examples/test.project b/inst/examples/test.project
@@ -39,7 +39,6 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no

diff --git a/inst/examples/tests/iris.project b/inst/examples/tests/iris.project
@@ -38,7 +38,6 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no

diff --git a/inst/examples/train_data.project b/inst/examples/train_data.project
@@ -37,7 +37,6 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
 PrintPerformance=yes
 PrintSets=no
 SavePartitions=no

diff --git a/inst/settings/template.project b/inst/settings/template.project
@@ -38,13 +38,12 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutOffsetsBestLength=no
-PrintPerformance=yes
+PrintPerformance=no
 PrintSets=no
 SavePartitions=no
 [Run]
 Subsumption=no
 BranchBound=yes
 Parallel=yes
-ParallelMethod=ONE
+ParallelMethod=TWO
 BinaryReduction=no
diff --git a/man/modelsCurveExplore.Rd b/man/modelsCurveExplore.Rd
diff --git a/man/settingsExplore.Rd b/man/settingsExplore.Rd
diff --git a/man/trainExplore.Rd b/man/trainExplore.Rd
diff --git a/tests/testthat/test-MainFunctions.R b/tests/testthat/test-MainFunctions.R
@@ -110,3 +110,60 @@ test_that("compute AUC", {
   expect_true(auroc < 100)
   expect_true(auroc > 0)
 })
+
+test_that("mandatory features", {
+  ### Tests for EXPLORE using iris dataset
+  data_path <- system.file("examples", "tests", "iris.arff", package = "Explore")
+  settings_path <- system.file("examples", "tests", "iris.project", package = "Explore")
+  output_path <- paste0(tempdir(), "/", "Test1")
+  dir.create(output_path)
+  if (.Platform$OS.type == "windows") {
+    output_path <- gsub("\\\\", "/", output_path)
+  }
+  output_path <- paste0(output_path, "/")
+  data <- farff::readARFF(data_path)
+  model <- Explore::trainExplore(output_path = output_path,
+                                 file_name = "iris",
+                                 train_data = data,
+                                 ClassFeature = "'class'",
+                                 PositiveClass = '"Iris-versicolor"',
+                                 FeatureInclude = "'sepalwidth';'sepallength'")
+  expect_equal(class(model), "character")
+  # expect_true(is.na(model), info = "Test failed because model is NA")
+  expect_equal(model, "'sepallength'>4.9AND'sepalwidth'<=3.2AND'petalwidth'<=1.7")
+})
+
+test_that("balanced accuracy constraint ", {
+  data_path <- system.file("examples", "complexity", "mix_4.arff", package = "Explore")
+  output_path <- paste0(getwd(), "/", "Test1")
+  dir.create(output_path)
+  if (.Platform$OS.type == "windows") {
+    output_path <- gsub("\\\\", "/", output_path)
+  }
+  output_path <- paste0(output_path, "/")
+
+  data <- farff::readARFF(data_path)
+  data <-as.data.frame(apply(data,2,as.numeric))
+
+  model_without <- Explore::trainExplore(output_path = output_path,
+                                 file_name = "mix_4",
+                                 train_data = data,
+                                 StartRulelength = 3,
+                                 ClassFeature = "'outcomeCount'",
+                                 PositiveClass = '"1"')
+  num_without <- Explore::candidatesExplore(paste0(output_path, "mix_4", ".result"))
+
+  model_with <- Explore::trainExplore(output_path = output_path,
+                                         file_name = "mix_4",
+                                         train_data = data,
+                                         StartRulelength = 3,
+                                         ClassFeature = "'outcomeCount'",
+                                         PositiveClass = '"1"',
+                                         BalancedAccuracy = 0.6,
+                                         OutputMethod = "EVERY",
+                                         Parallel = FALSE)
+  num_with <- Explore::candidatesExplore(paste0(output_path, "mix_4", ".result"))
+
+  expect_equal(num_without, 1940)
+  expect_equal(num_with, 36)
+})