Release version 2.0.0

.Rbuildignore

@@ -17,3 +17,5 @@
 ^tests/testthat/Rplots\.pdf$
 ^tests/old_experiments$
 ^Rplots\.pdf$
+^\.positai$
+^\.claude$

.gitignore

@@ -9,3 +9,4 @@ tests/testthat/Rplots.pdf
 /Meta/
 tests/old_experiments/_experiment
 Rplots.pdf
+.positai

.lintr

@@ -1,7 +1,28 @@
 linters: linters_with_defaults(
+    any_duplicated_linter(),
+    any_is_na_linter(),
+    boolean_arithmetic_linter(),
+    class_equals_linter(),
+    commented_code_linter = NULL,
+    duplicate_argument_linter(),
+    empty_assignment_linter(),
+    for_loop_index_linter(),
+    function_left_parentheses_linter(),
+    function_return_linter(),
+    implicit_assignment_linter(),
+    implicit_integer_linter(),
+    length_levels_linter(),
+    length_test_linter(),
+    lengths_linter(),
     line_length_linter(120),
+    missing_argument_linter(),
+    numeric_leading_zero_linter(),
     object_length_linter = NULL,
-    trailing_whitespace_linter = NULL,
-    cyclocomp_linter = NULL
+    object_name_linter = NULL,
+    outer_negation_linter(),
+    paste_linter(),
+    return_linter = NULL,
+    todo_comment_linter(),
+    trailing_whitespace_linter = NULL
   )
 encoding: "UTF-8"

DESCRIPTION

@@ -1,18 +1,14 @@
 Package: familiar
 Title: End-to-End Automated Machine Learning and Model Evaluation
-Version: 1.5.0
+Version: 2.0.0
 Authors@R: c(
     person("Alex", "Zwanenburg",
            email = "alexander.zwanenburg@nct-dresden.de",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0342-9545")),
     person("Steffen", "Löck", role="aut"),
-    person("Stefan", "Leger", role="ctb"),
-    person("Iram", "Shahzadi", role="ctb"),
-    person("Asier", "Rabasco Meneghetti", role="ctb"),
-    person("Sebastian", "Starke", role="ctb"),
-    person("Technische Universität Dresden", role="cph"),
-    person("German Cancer Research Center (DKFZ)", role="cph"))
+    person("German Cancer Research Center (DKFZ)", role="cph"),
+    person("Technische Universität Dresden", role="cph"))
 Description: Single unified interface for end-to-end modelling of regression, 
     categorical and time-to-event (survival) outcomes. Models created using
     familiar are self-containing, and their use does not require additional
@@ -24,19 +20,19 @@ Description: Single unified interface for end-to-end modelling of regression,
     tabular format and plotted, and may also be computed manually using export
     and plot functions. Where possible, metrics and values obtained during the
     evaluation process come with confidence intervals.
-URL: https://github.com/alexzwanenburg/familiar
-BugReports: https://github.com/alexzwanenburg/familiar/issues
+URL: https://github.com/oncoray/familiar
+BugReports: https://github.com/oncoray/familiar/issues
 Depends: R (>= 4.0.0)
 License: EUPL
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Imports:
     data.table,
     methods,
-    rlang (>= 0.3.4),
+    rlang (>= 1.0.0),
     rstream,
     survival
 Suggests:
@@ -47,35 +43,30 @@ Suggests:
     coro,
     dynamicTreeCut,
     e1071 (>= 1.7.5),
-    Ecdat,
     fastcluster,
     fastglm,
-    ggplot2 (>= 3.0.0),
+    ggplot2 (>= 4.0.0),
     glmnet,
     gtable,
     harmonicmeanp,
-    isotree (>= 0.3.0),
+    isotree (>= 0.6.0),
     knitr,
     labeling,
     laGP,
-    MASS,
     maxstat,
-    mboost (>= 2.9.0),
     microbenchmark,
     nnet,
-    partykit,
+    paletteer,
     power.transform,
     praznik,
     proxy,
-    qvalue,
     randomForestSRC,
     ranger,
     rmarkdown,
     scales,
     testthat (>= 3.0.0),
     xml2,
-    VGAM,
-    xgboost
+    xgboost (>= 3.0.0)
 Collate: 
     'FamiliarS4Classes.R'
     'FamiliarS4Generics.R'
@@ -97,14 +88,15 @@ Collate:
     'DataProcessing.R'
     'DataServerBackend.R'
     'ErrorMessages.R'
-    'Evaluation.R'
     'ExperimentData.R'
     'ExperimentSetup.R'
     'Familiar.R'
     'FamiliarCollection.R'
     'FamiliarCollectionExport.R'
     'FamiliarData.R'
     'FamiliarDataComputation.R'
+    'FamiliarDataComputationPredictionData.R'
+    'PredictionTable.R'
     'FamiliarDataComputationAUCCurves.R'
     'FamiliarDataComputationCalibrationData.R'
     'FamiliarDataComputationCalibrationInfo.R'
@@ -116,11 +108,12 @@ Collate:
     'FamiliarDataComputationICE.R'
     'FamiliarDataComputationModelPerformance.R'
     'FamiliarDataComputationPermutationVimp.R'
-    'FamiliarDataComputationPredictionData.R'
     'FamiliarDataComputationRiskStratificationData.R'
     'FamiliarDataComputationRiskStratificationInfo.R'
+    'FamiliarDataComputationSHAP.R'
     'FamiliarDataComputationSampleSimilarity.R'
     'FamiliarDataComputationUnivariateAnalysis.R'
+    'FamiliarDataComputationUtilities.R'
     'FamiliarDataComputationVimp.R'
     'FamiliarDataElement.R'
     'FamiliarEnsemble.R'
@@ -134,7 +127,6 @@ Collate:
     'FamiliarVimpMethod.R'
     'FeatureInfo.R'
     'FeatureInfoParameters.R'
-    'FeatureSelection.R'
     'FunctionWrapperUtilities.R'
     'HyperparameterOptimisation.R'
     'HyperparameterOptimisationMetaLearners.R'
@@ -147,6 +139,7 @@ Collate:
     'Iterations.R'
     'LearnerMain.R'
     'LearnerRecalibration.R'
+    'LearnerRiskStratification.R'
     'LearnerS4Cox.R'
     'LearnerS4GLM.R'
     'LearnerS4GLMnet.R'
@@ -158,7 +151,6 @@ Collate:
     'LearnerS4SVM.R'
     'LearnerS4SurvivalRegression.R'
     'LearnerS4XGBoost.R'
-    'LearnerSurvivalGrouping.R'
     'LearnerSurvivalProbability.R'
     'Logger.R'
     'MetricS4.R'
@@ -167,9 +159,8 @@ Collate:
     'MetricS4ConcordanceIndex.R'
     'MetricS4ConfusionMatrixMetrics.R'
     'MetricS4Regression.R'
-    'ModelBuilding.R'
-    'NoveltyDetectorS4IsolationTree.R'
     'NoveltyDetectorMain.R'
+    'NoveltyDetectorS4IsolationTree.R'
     'NoveltyDetectorS4NoneNoveltyDetector.R'
     'OutcomeInfo.R'
     'PairwiseSimilarity.R'
@@ -182,6 +173,7 @@ Collate:
     'PlotColours.R'
     'PlotConfusionMatrix.R'
     'PlotDecisionCurves.R'
+    'PlotFamiliarPlot.R'
     'PlotFeatureRanking.R'
     'PlotFeatureSimilarity.R'
     'PlotGTable.R'
@@ -191,21 +183,36 @@ Collate:
     'PlotModelPerformance.R'
     'PlotPermutationVariableImportance.R'
     'PlotSampleClustering.R'
+    'PlotShapDependence.R'
+    'PlotShapForce.R'
+    'PlotShapSummary.R'
+    'PlotShapWaterfall.R'
     'PlotUnivariateImportance.R'
     'PlotUtilities.R'
     'PredictS4Methods.R'
     'ProcessTimeUtilities.R'
     'Random.R'
-    'RandomGrouping.R'
     'RankBordaAggregation.R'
     'RankMain.R'
     'RankSimpleAggregation.R'
     'RankStabilityAggregation.R'
     'SocketServer.R'
     'StringUtilities.R'
+    'TaskEvaluate.R'
+    'TaskFeatureInfo.R'
+    'TaskLearn.R'
+    'TaskLearnerHyperparameters.R'
+    'TaskMain.R'
+    'TaskNoveltyDetector.R'
+    'TaskNoveltyDetectorHyperparameters.R'
+    'TaskVimp.R'
+    'TaskVimpHyperparameters.R'
     'TestDataCreators.R'
+    'TestFeatureInfo.R'
     'TestFunctions.R'
-    'TrainS4Methods.R'
+    'TestTrain.R'
+    'TestTrainNovelty.R'
+    'TestVimp.R'
     'TrimUtilities.R'
     'Utilities.R'
     'UtilitiesS4.R'

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(as_prediction_table)
 export(coef)
 export(get_xml_config)
 export(plot_feature_selection_occurrence)
@@ -56,9 +57,9 @@ exportMethods(export_univariate_analysis_data)
 exportMethods(get_class_names)
 exportMethods(get_data_set_names)
 exportMethods(get_feature_names)
-exportMethods(get_fs_method_names)
 exportMethods(get_learner_names)
 exportMethods(get_risk_group_names)
+exportMethods(get_vimp_method_names)
 exportMethods(get_vimp_table)
 exportMethods(plot_auc_precision_recall_curve)
 exportMethods(plot_auc_roc_curve)
@@ -71,21 +72,26 @@ exportMethods(plot_kaplan_meier)
 exportMethods(plot_model_performance)
 exportMethods(plot_permutation_variable_importance)
 exportMethods(plot_sample_clustering)
+exportMethods(plot_shap_dependence)
+exportMethods(plot_shap_force)
+exportMethods(plot_shap_summary)
+exportMethods(plot_shap_waterfall)
 exportMethods(plot_univariate_importance)
 exportMethods(plot_variable_importance)
 exportMethods(predict)
 exportMethods(set_class_names)
 exportMethods(set_data_set_names)
 exportMethods(set_feature_names)
-exportMethods(set_fs_method_names)
 exportMethods(set_learner_names)
 exportMethods(set_risk_group_names)
+exportMethods(set_vimp_method_names)
 exportMethods(summary)
 exportMethods(update_model_dir_path)
 exportMethods(update_object)
 import(data.table)
 import(methods)
 importClassesFrom(rstream,rstream.runif)
+importFrom(rlang,"%<~%")
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,ensym)