├── .Rbuildignore ├── .github ├── .gitignore ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug.yml │ ├── config.yml │ └── feature_request.yml └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE.note ├── NAMESPACE ├── NEWS.md ├── R ├── ANN-class.R ├── BRT-class.R ├── Maxent-class.R ├── Maxnet-class.R ├── RF-class.R ├── RcppExports.R ├── SDMmodel-class.R ├── SDMmodel2MaxEnt.R ├── SDMmodelCV-class.R ├── SDMtune-class.R ├── SDMtune-package.R ├── SWD-class.R ├── addSamplesToBg.R ├── aicc.R ├── auc.R ├── chart-utils.R ├── checkMaxentInstallation.R ├── combineCV.R ├── confMatrix.R ├── convertFolds.R ├── corVar.R ├── doJk.R ├── getTunableArgs.R ├── gridSearch.R ├── maxentTh.R ├── maxentVarImp.R ├── mergeSWD.R ├── modelReport.R ├── optimizeModel.R ├── plotCor.R ├── plotJk.R ├── plotPA.R ├── plotPred.R ├── plotROC.R ├── plotResponse.R ├── plotVarImp.R ├── predict-ANN.R ├── predict-BRT.R ├── predict-Maxent.R ├── predict-Maxnet.R ├── predict-RF.R ├── predict-SDMmodel.R ├── predict-SDMmodelCV.R ├── prepareSWD.R ├── randomFolds.R ├── randomSearch.R ├── reduceVar.R ├── swd2csv.R ├── sysdata.rda ├── thinData.R ├── thresholds.R ├── train.R ├── trainANN.R ├── trainBRT.R ├── trainMaxent.R ├── trainMaxnet.R ├── trainRF.R ├── trainValTest.R ├── tss.R ├── utils.R ├── varImp.R ├── varSel.R ├── virtualSp.R └── zzz.R ├── README.Rmd ├── README.md ├── SDMtune.Rproj ├── codecov.yml ├── cran-comments.md ├── data-raw ├── sysdata.R └── virtualSp.R ├── data └── virtualSp.rda ├── inst ├── CITATION ├── WORDLIST ├── lib │ ├── Chart.min.js │ ├── jquery.min.js │ └── style.css ├── scripts │ ├── gridSearch.js │ ├── optimizeModel.js │ └── varSelection.js └── templates │ ├── chart_template.html │ ├── modelReport.Rmd │ └── report.css ├── man ├── ANN-class.Rd ├── BRT-class.Rd ├── Maxent-class.Rd ├── Maxnet-class.Rd ├── RF-class.Rd ├── SDMmodel-class.Rd ├── SDMmodel2MaxEnt.Rd ├── SDMmodelCV-class.Rd ├── SDMtune-class.Rd ├── SDMtune-package.Rd ├── SWD-class.Rd ├── addSamplesToBg.Rd ├── aicc.Rd ├── auc.Rd ├── checkMaxentInstallation.Rd ├── combineCV.Rd ├── confMatrix.Rd ├── corVar.Rd ├── doJk.Rd ├── figures │ ├── bench.png │ ├── logo.png │ └── realtime-chart.gif ├── getTunableArgs.Rd ├── gridSearch.Rd ├── maxentTh.Rd ├── maxentVarImp.Rd ├── mergeSWD.Rd ├── modelReport.Rd ├── optimizeModel.Rd ├── plotCor.Rd ├── plotJk.Rd ├── plotPA.Rd ├── plotPred.Rd ├── plotROC.Rd ├── plotResponse.Rd ├── plotVarImp.Rd ├── predict-ANN-method.Rd ├── predict-BRT-method.Rd ├── predict-Maxent-method.Rd ├── predict-Maxnet-method.Rd ├── predict-RF-method.Rd ├── predict-SDMmodel-method.Rd ├── predict-SDMmodelCV-method.Rd ├── prepareSWD.Rd ├── randomFolds.Rd ├── randomSearch.Rd ├── reduceVar.Rd ├── swd2csv.Rd ├── thinData.Rd ├── thresholds.Rd ├── train.Rd ├── trainValTest.Rd ├── tss.Rd ├── varImp.Rd ├── varSel.Rd └── virtualSp.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── src ├── RcppExports.cpp └── utils.cpp ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── ANN-class.md │ ├── BRT-class.md │ ├── Maxent-class.md │ ├── Maxnet-class.md │ ├── RF-class.md │ ├── SDMmodel-class.md │ ├── SDMmodel2MaxEnt.md │ ├── SDMmodelCV-class.md │ ├── SDMtune-class.md │ ├── SWD-class.md │ ├── addSamplesToBg.md │ ├── aicc.md │ ├── auc.md │ ├── checkMaxentInstallation.md │ ├── confMatrix.md │ ├── convertFolds.md │ ├── corVar.md │ ├── doJk.md │ ├── gridSearch.md │ ├── maxentTh.md │ ├── maxentVarImp.md │ ├── mergeSWD.md │ ├── modelReport.md │ ├── optimizeModel.md │ ├── plotJk.md │ ├── plotPA.md │ ├── plotPred.md │ ├── predict-SDMmodel.md │ ├── predict-SDMmodelCV.md │ ├── prepareSWD.md │ ├── randomFolds.md │ ├── reduceVar.md │ ├── swd2csv.md │ ├── thinData.md │ ├── trainMaxent.md │ ├── trainValTest.md │ ├── tss.md │ ├── utils.md │ └── varSel.md │ ├── helper.R │ ├── setup.R │ ├── test-ANN-class.R │ ├── test-BRT-class.R │ ├── test-Maxent-class.R │ ├── test-Maxnet-class.R │ ├── test-RF-class.R │ ├── test-SDMmodel-class.R │ ├── test-SDMmodel2MaxEnt.R │ ├── test-SDMmodelCV-class.R │ ├── test-SDMtune-class.R │ ├── test-SWD-class.R │ ├── test-addSamplesToBg.R │ ├── test-aicc.R │ ├── test-auc.R │ ├── test-chart-utils.R │ ├── test-checkMaxentInstallation.R │ ├── test-clamp.R │ ├── test-combineCV.R │ ├── test-confMatrix.R │ ├── test-convertFolds.R │ ├── test-corVar.R │ ├── test-doJk.R │ ├── test-getTunableArgs.R │ ├── test-gridSearch.R │ ├── test-maxentTh.R │ ├── test-maxentVarImp.R │ ├── test-mergeSWD.R │ ├── test-modelReport.R │ ├── test-optimizeModel.R │ ├── test-plotCor.R │ ├── test-plotJk.R │ ├── test-plotPA.R │ ├── test-plotPred.R │ ├── test-plotROC.R │ ├── test-plotResponse.R │ ├── test-plotVarImp.R │ ├── test-predct-Maxnet.R │ ├── test-predict-ANN.R │ ├── test-predict-BRT.R │ ├── test-predict-Maxent.R │ ├── test-predict-RF.R │ ├── test-predict-SDMmodel.R │ ├── test-predict-SDMmodelCV.R │ ├── test-prepareSWD.R │ ├── test-randomFolds.R │ ├── test-randomSearch.R │ ├── test-reduceVar.R │ ├── test-swd2csv.R │ ├── test-thinData.R │ ├── test-thresholds.R │ ├── test-train.R │ ├── test-trainANN.R │ ├── test-trainBRT.R │ ├── test-trainMaxent.R │ ├── test-trainMaxnet.R │ ├── test-trainRF.R │ ├── test-trainValTest.R │ ├── test-tss.R │ ├── test-utils.R │ ├── test-varImp.R │ └── test-varSel.R └── vignettes ├── SDMtune.bib ├── articles ├── evaluate-model.Rmd ├── evaluation-strategies.Rmd ├── make-predictions.Rmd ├── prepare-data.Rmd ├── train-model.Rmd ├── train-tune-presence-absence-models.Rmd ├── tune-hyperparameters.Rmd ├── variable-importance.Rmd └── variable-selection.Rmd ├── basic-use.Rmd ├── hyper-tuning.Rmd ├── presence-absence.Rmd └── var-selection.Rmd /.Rbuildignore: 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