├── .Rbuildignore ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── Misc.R ├── aggregateTaxa.R ├── aggregateTaxa_coarse.R ├── aggregateTaxa_fine.R ├── changeDecisionsDummies.R ├── decisionImportance.R ├── decisions2FullDummy.R ├── discretizeData.R ├── discretizeData_model.R ├── discretizeDecisions.R ├── discretizeVector.R ├── discretizeVector_model.R ├── endoR.R ├── evaluateAlpha.R ├── featureImportance.R ├── filterDecisionsImportances.R ├── getComplements.R ├── getDecisionsMetric.R ├── getNetwork.R ├── getThresholds.R ├── measureSingleDecision.R ├── model2DE.R ├── model2DE_cluster.R ├── model2DE_resampling.R ├── plotFeatures.R ├── plotNetwork.R ├── preCluster.R ├── pruneDecisions.R ├── scripts_from_inTrees.R └── stabilitySelection.R ├── README.md ├── cran-comments.md ├── data └── titanic.rda ├── endoR.Rcheck ├── 00_pkg_src │ └── endoR │ │ ├── .github │ │ └── workflows │ │ │ └── ci.yml │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── R │ │ ├── Misc.R │ │ ├── aggregateTaxa.R │ │ ├── aggregateTaxa_coarse.R │ │ ├── aggregateTaxa_fine.R │ │ ├── changeDecisionsDummies.R │ │ ├── decisionImportance.R │ │ ├── decisions2FullDummy.R │ │ ├── discretizeData.R │ │ ├── discretizeData_model.R │ │ ├── discretizeDecisions.R │ │ ├── discretizeVector.R │ │ ├── discretizeVector_model.R │ │ ├── endoR.R │ │ ├── evaluateAlpha.R │ │ ├── featureImportance.R │ │ ├── filterDecisionsImportances.R │ │ ├── getComplements.R │ │ ├── getDecisionsMetric.R │ │ ├── getNetwork.R │ │ ├── getThresholds.R │ │ ├── measureSingleDecision.R │ │ ├── model2DE.R │ │ ├── model2DE_cluster.R │ │ ├── model2DE_resampling.R │ │ ├── plotFeatures.R │ │ ├── plotNetwork.R │ │ ├── preCluster.R │ │ ├── pruneDecisions.R │ │ ├── scripts_from_inTrees.R │ │ └── stabilitySelection.R │ │ ├── README.md │ │ ├── build │ │ └── vignette.rds │ │ ├── data │ │ └── titanic.rda │ │ ├── figures │ │ ├── Decisions_summary.png │ │ └── Workflow.png │ │ ├── man │ │ ├── aggregateTaxa.Rd │ │ ├── compatibleNames.Rd │ │ ├── decisionImportance.Rd │ │ ├── decisions2FullDummy.Rd │ │ ├── discretizeData.Rd │ │ ├── discretizeData_model.Rd │ │ ├── discretizeDecisions.Rd │ │ ├── endoR.Rd │ │ ├── evaluateAlpha.Rd │ │ ├── featureImportance.Rd │ │ ├── filterDecisionsImportances.Rd │ │ ├── getDecisionsMetrics.Rd │ │ ├── getNetwork.Rd │ │ ├── getThresholds.Rd │ │ ├── model2DE.Rd │ │ ├── model2DE_cluster.Rd │ │ ├── model2DE_resampling.Rd │ │ ├── plotFeatures.Rd │ │ ├── plotNetwork.Rd │ │ ├── preCluster.Rd │ │ ├── pruneDecisions.Rd │ │ └── stabilitySelection.Rd │ │ ├── tests │ │ ├── testthat.R │ │ └── testthat │ │ │ └── test-test.R │ │ └── vignettes │ │ ├── iris_multiclass.Rmd │ │ ├── iris_multiclass.ipynb │ │ ├── titanic_bootstraps.Rmd │ │ └── titanic_bootstraps.ipynb ├── 00check.log └── R_check_bin │ ├── R │ └── Rscript ├── endoR.Rproj ├── endoR_0.1.0.tar.gz ├── examples ├── iris_basic.R ├── iris_bootstraps.R └── iris_each_function.R ├── figure ├── unnamed-chunk-14-1.png ├── unnamed-chunk-16-1.png ├── unnamed-chunk-17-1.png ├── unnamed-chunk-18-1.png ├── unnamed-chunk-25-1.png └── unnamed-chunk-26-1.png ├── figures ├── Decisions_summary.png └── Workflow.png ├── man ├── aggregateTaxa.Rd ├── changeDecisionsDummies.Rd ├── compatibleNames.Rd ├── decisionImportance.Rd ├── decisions2FullDummy.Rd ├── discretizeData.Rd ├── discretizeData_model.Rd ├── discretizeDecisions.Rd ├── endoR.Rd ├── evaluateAlpha.Rd ├── featureImportance.Rd ├── filterDecisionsImportances.Rd ├── getDecisionsMetrics.Rd ├── getNetwork.Rd ├── getThresholds.Rd ├── model2DE.Rd ├── model2DE_cluster.Rd ├── model2DE_resampling.Rd ├── plotFeatures.Rd ├── plotNetwork.Rd ├── preCluster.Rd ├── pruneDecisions.Rd ├── stabilitySelection.Rd └── titanic.Rd ├── tests ├── testthat.R └── testthat │ └── test-test.R └── vignettes ├── iris_multiclass.Rmd ├── iris_multiclass.ipynb ├── titanic_bootstraps.Rmd ├── titanic_bootstraps.Rmd.orig └── titanic_bootstraps.ipynb /.Rbuildignore: 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