Files in hxia/plp-git-demo

Package for patient level prediction using data in the OMOP Common Data Model

DESCRIPTION

NAMESPACE

NEWS.md

PatientLevelPrediction.Rproj

R/AdaBoost.R R/AndromedaHelperFunctions.R R/ApplyPlp.R R/AttritionDiagramPlp.R R/CIReNN.R R/CNNTorch.R R/CovNN.R R/CovNN2.R R/CoxModel.R R/CreatePlpDocument.R R/DataSplitting.R R/DecisionTree.R R/DeepNN.R R/Diagnostics.R R/Ensemble.R R/EvaluatePlp.R R/ExternalValidatePlp.R R/FeatureImportance.R R/Fit.R R/FitGLMModel.R R/Formatting.R R/GBMSurvival.R R/GradientBoostingMachine.R R/HelperFunctions.R R/ImportExport.R R/KNN.R R/LRTorch.R R/LassoLogisticRegression.R R/LearningCurve.R R/MLP.R R/MLPTorch.R R/NaiveBayes.R R/Parallel.R R/ParamChecks.R R/PatientLevelPrediction.R R/Plotting.R R/Predict.R R/RNNTorch.R R/RandomForest.R R/RandomForestQuantileRegressor.R R/RcppExports.R R/RunMultiplePlp.R R/RunPlp.R R/SVM.R R/SageMakerBinary.R R/SaveLoadPlp.R R/Shiny.R R/Simulation.R R/StudyPopulation.R R/ViewShinyPlp.R README.md

_pkgdown.yml

compare_versions

data/plpDataSimulationProfile.rda

demo/00Index

demo/EnsembleModelDemo.R demo/LearningCurveDemo.R demo/SingleModelDemo.R

deploy.sh

docs/404.html

docs/articles/ATLAS_O.png

docs/articles/ATLAS_T.png

docs/articles/AddingCustomAlgorithms.html

docs/articles/AddingExistingModels.html

docs/articles/BuildingDeepLearningModels.html

docs/articles/BuildingEnsembleModels.html

docs/articles/BuildingMultiplePredictiveModels.html

docs/articles/BuildingPredictiveModels.html

docs/articles/CreatingNetworkStudies.html

docs/articles/CreatingShinyApp.html

docs/articles/CustomPredictionAlgorithms.html

docs/articles/Figure1.png

docs/articles/GeneratingLearningCurves.html

docs/articles/ImplementingExistingModels.html

docs/articles/InstallationGuide.html

docs/articles/PatientLevelPrediction.html

docs/articles/PlottingLearningCurves.html

docs/articles/Videos.html

docs/articles/arch1.png

docs/articles/atlasdownload1.png

docs/articles/atlasdownload2.png

docs/articles/atlasplp1.png

docs/articles/atlasplp2.png

docs/articles/atlasplp3.png

docs/articles/atlasplp4.png

docs/articles/cirenn.png

docs/articles/cnn_lstm.png

docs/articles/cnn_mlf2.png

docs/articles/conv_arch1.png

docs/articles/conv_arch2.png

docs/articles/covcnn.png

docs/articles/covcnn2.png

docs/articles/demographicSummary.png

docs/articles/ensemble.png

docs/articles/example1/ATLAS_O.png

docs/articles/example1/ATLAS_T.png

docs/articles/example2/aceinhibitors.png

docs/articles/example2/angioedema.png

docs/articles/generalizability.png

docs/articles/index.html

docs/articles/learningCurve.png

docs/articles/learningCurveBias.png

docs/articles/learningCurvePlot.png

docs/articles/learningCurveVariance.png

docs/articles/lstm_last.png

docs/articles/popdef1.png

docs/articles/popdef2.png

docs/articles/popdef3.png

docs/articles/popdef4.png

docs/articles/popdef5.png

docs/articles/popdef6.png

docs/articles/precisionRecall.png

docs/articles/predictionDistribution.png

docs/articles/preferencePDF.png

docs/articles/problems.png

docs/articles/shinyroc.png

docs/articles/shinysummary.png

docs/articles/smoothCalibration.jpeg

docs/articles/sparseCalibration.png

docs/articles/sparseRoc.png

docs/articles/studydesign.png

docs/articles/variableScatterplot.png

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/PatientLevelPrediction.html

docs/reference/accuracy.html

docs/reference/applyEnsembleModel.html

docs/reference/applyModel.html

docs/reference/averagePrecision.html

docs/reference/brierScore.html

docs/reference/bySumFf.html

docs/reference/calibrationLine.html

docs/reference/checkPlpInstallation.html

docs/reference/checkffFolder.html

docs/reference/clearffTempDir.html

docs/reference/combinePlpModelSettings.html

docs/reference/computeAuc.html

docs/reference/computeAucFromDataFrames.html

docs/reference/configurePython.html

docs/reference/createExistingModelSql.html

docs/reference/createLearningCurve.html

docs/reference/createLearningCurvePar.html

docs/reference/createLrSql.html

docs/reference/createPlpJournalDocument.html

docs/reference/createPlpModelSettings.html

docs/reference/createPlpReport.html

docs/reference/createStudyPopulation.html

docs/reference/createStudyPopulationSettings.html

docs/reference/diagnostic.html

docs/reference/diagnosticOddsRatio.html

docs/reference/drawAttritionDiagramPlp.html

docs/reference/evaluateExistingModel.html

docs/reference/evaluateMultiplePlp.html

docs/reference/evaluatePlp.html

docs/reference/exportPlpDataToCsv.html

docs/reference/externalValidatePlp.html

docs/reference/f1Score.html

docs/reference/falseDiscoveryRate.html

docs/reference/falseNegativeRate.html

docs/reference/falseOmissionRate.html

docs/reference/falsePositiveRate.html

docs/reference/fitGLMModel.html

docs/reference/fitPlp.html

docs/reference/getAttritionTable.html

docs/reference/getCalibration.html

docs/reference/getCovariateData.html

docs/reference/getModelDetails.html

docs/reference/getPlpData.html

docs/reference/getPlpTable.html

docs/reference/getPredictionDistribution.html

docs/reference/getThresholdSummary.html

docs/reference/grepCovariateNames.html

docs/reference/index.html

docs/reference/insertDbPopulation.html

docs/reference/interpretInstallCode.html

docs/reference/launchDiagnosticsExplorer.html

docs/reference/listAppend.html

docs/reference/loadEnsemblePlpModel.html

docs/reference/loadEnsemblePlpResult.html

docs/reference/loadPlpData.html

docs/reference/loadPlpModel.html

docs/reference/loadPlpResult.html

docs/reference/loadPrediction.html

docs/reference/loadPredictionAnalysisList.html

docs/reference/negativeLikelihoodRatio.html

docs/reference/negativePredictiveValue.html

docs/reference/outcomeSurvivalPlot.html

docs/reference/personSplitter.html

docs/reference/plotDemographicSummary.html

docs/reference/plotF1Measure.html

docs/reference/plotGeneralizability.html

docs/reference/plotLearningCurve.html

docs/reference/plotPlp.html

docs/reference/plotPrecisionRecall.html

docs/reference/plotPredictedPDF.html

docs/reference/plotPredictionDistribution.html

docs/reference/plotPreferencePDF.html

docs/reference/plotRoc.html

docs/reference/plotSmoothCalibration.html

docs/reference/plotSparseCalibration.html

docs/reference/plotSparseCalibration2.html

docs/reference/plotSparseRoc.html

docs/reference/plotVariableScatterplot.html

docs/reference/plpDataSimulationProfile.html

docs/reference/positiveLikelihoodRatio.html

docs/reference/positivePredictiveValue.html

docs/reference/predictAndromeda.html

docs/reference/predictFfdf.html

docs/reference/predictPlp.html

docs/reference/predictProbabilities.html

docs/reference/randomSplitter.html

docs/reference/registerParallelBackend.html

docs/reference/registerSequentialBackend.html

docs/reference/runEnsembleModel.html

docs/reference/runPlp.html

docs/reference/runPlpAnalyses.html

docs/reference/saveEnsemblePlpModel.html

docs/reference/saveEnsemblePlpResult.html

docs/reference/savePlpData.html

docs/reference/savePlpModel.html

docs/reference/savePlpResult.html

docs/reference/savePrediction.html

docs/reference/savePredictionAnalysisList.html

docs/reference/sensitivity.html

docs/reference/setAdaBoost.html

docs/reference/setCIReNN.html

docs/reference/setCNNTorch.html

docs/reference/setCovNN.html

docs/reference/setCovNN2.html

docs/reference/setCoxModel.html

docs/reference/setDecisionTree.html

docs/reference/setDeepNN.html

docs/reference/setGBMSurvival.html

docs/reference/setGradientBoostingMachine.html

docs/reference/setKNN.html

docs/reference/setLRTorch.html

docs/reference/setLassoLogisticRegression.html

docs/reference/setMLP.html

docs/reference/setMLPTorch.html

docs/reference/setNaiveBayes.html

docs/reference/setPythonEnvironment.html

docs/reference/setRNNTorch.html

docs/reference/setRNNTorch2.html

docs/reference/setRandomForest.html

docs/reference/setRandomForestQuantileRegressor.html

docs/reference/setSagemakerBinary.html

docs/reference/similarPlpData.html

docs/reference/simulatePlpData.html

docs/reference/specificity.html

docs/reference/subjectSplitter.html

docs/reference/summaryPlpAnalyses.html

docs/reference/timeSplitter.html

docs/reference/toPlpData.html

docs/reference/toSparseM.html

docs/reference/toSparsePython.html

docs/reference/toSparseTorchPython.html

docs/reference/toSparseTorchPython2.html

docs/reference/transferLearning.html

docs/reference/transportModel.html

docs/reference/transportPlp.html

docs/reference/viewMultiplePlp.html

docs/reference/viewPlp.html

extras/PackageMaintenance.R extras/PatientLevelPrediction.pdf extras/SimulationDataFetch.R extras/TestLearningCurve.R extras/VignetteDataFetch.R extras/getProtocolSpecification.R

inst/CITATION

inst/doc/AddingCustomAlgorithms.pdf

inst/doc/AddingCustomAlgorithms.tex

inst/doc/BuildingDeepLearningModels.pdf

inst/doc/BuildingDeepLearningModels.tex

inst/doc/BuildingEnsembleModels.pdf

inst/doc/BuildingEnsembleModels.tex

inst/doc/BuildingMultiplePredictiveModels.pdf

inst/doc/BuildingMultiplePredictiveModels.tex

inst/doc/BuildingPredictiveModels.pdf

inst/doc/BuildingPredictiveModels.tex

inst/doc/CreatingLearningCurves.pdf

inst/doc/CreatingLearningCurves.tex

inst/doc/CreatingNetworkstudies.pdf

inst/doc/CreatingNetworkstudies.tex

inst/doc/CreatingShinyApp.pdf

inst/doc/CreatingShinyApp.tex

inst/doc/Figure1.png

inst/doc/InstallationGuide.pdf

inst/doc/InstallationGuide.tex

inst/python/TorchMap.py

inst/python/TorchUtils.py

inst/python/adaBoostFunctions.py

inst/python/decisionTreeFunctions.py

inst/python/deepTorch.py

inst/python/deepTorchFunctions.py

inst/python/gardenFunctions.py

inst/python/gbmSurvivalFunctions.py

inst/python/mlpFunctions.py

inst/python/naiveBayesFunctions.py

inst/python/predictFunctions.py

inst/python/python_predict.py

inst/python/randomForestFunctions.py

inst/python/sageMakerFunctions.py

inst/python/sageMakerPredict.py

inst/python/svmFunctions.py

inst/settings/rEnvironmentSnapshot.csv

inst/shiny/DiagnosticsExplorer/DiagnosticsExplorer.Rproj

inst/shiny/DiagnosticsExplorer/PlotsAndTables.R inst/shiny/DiagnosticsExplorer/global.R

inst/shiny/DiagnosticsExplorer/html/about.html

inst/shiny/DiagnosticsExplorer/html/characterizationInfo.html

inst/shiny/DiagnosticsExplorer/html/databases.html

inst/shiny/DiagnosticsExplorer/html/distributionInfo.html

inst/shiny/DiagnosticsExplorer/html/proportionInfo.html

inst/shiny/DiagnosticsExplorer/html/results.html

inst/shiny/DiagnosticsExplorer/server.R inst/shiny/DiagnosticsExplorer/ui.R

inst/shiny/DiagnosticsExplorer/www/favicon.ico

inst/shiny/DiagnosticsExplorer/www/logo.png

inst/shiny/PLPViewer/PLPViewer.Rproj

inst/shiny/PLPViewer/data/settings.csv

inst/shiny/PLPViewer/global.R inst/shiny/PLPViewer/helpers.R

inst/shiny/PLPViewer/html/DataInfo.html

inst/shiny/PLPViewer/html/Description.html

inst/shiny/PLPViewer/html/Help.html

inst/shiny/PLPViewer/html/Log.html

inst/shiny/PLPViewer/html/Model.html

inst/shiny/PLPViewer/html/Performance.html

inst/shiny/PLPViewer/html/Settings.html

inst/shiny/PLPViewer/html/Summary.html

inst/shiny/PLPViewer/html/boxHelp.html

inst/shiny/PLPViewer/html/calHelp.html

inst/shiny/PLPViewer/html/demoHelp.html

inst/shiny/PLPViewer/html/f1Help.html

inst/shiny/PLPViewer/html/prcHelp.html

inst/shiny/PLPViewer/html/predDistHelp.html

inst/shiny/PLPViewer/html/prefDistHelp.html

inst/shiny/PLPViewer/html/rocHelp.html

inst/shiny/PLPViewer/plots.R inst/shiny/PLPViewer/processing.R inst/shiny/PLPViewer/server.R inst/shiny/PLPViewer/ui.R

inst/shiny/PLPViewer/www/about.png

inst/shiny/PLPViewer/www/custom.css

inst/shiny/PLPViewer/www/dataInfo.md

inst/shiny/PLPViewer/www/favicon.ico

inst/shiny/PLPViewer/www/logo.png

inst/shiny/PLPViewer/www/shinyDescription.md

inst/sql/sql_server/CreateCohorts.sql

inst/sql/sql_server/GetCohorts.sql

inst/sql/sql_server/GetOutcomes.sql

inst/sql/sql_server/HospitalizationCohorts.sql

inst/sql/sql_server/RemoveCohortTempTables.sql

man-roxygen/GetCovarParams.R man/PatientLevelPrediction.Rd man/accuracy.Rd man/applyEnsembleModel.Rd man/applyModel.Rd man/averagePrecision.Rd man/brierScore.Rd man/calibrationLine.Rd man/checkPlpInstallation.Rd man/combinePlpModelSettings.Rd man/computeAuc.Rd man/computeAucFromDataFrames.Rd man/configurePython.Rd man/createLearningCurve.Rd man/createLearningCurvePar.Rd man/createLrSql.Rd man/createPlpJournalDocument.Rd man/createPlpModelSettings.Rd man/createPlpReport.Rd man/createStudyPopulation.Rd man/createStudyPopulationSettings.Rd man/diagnostic.Rd man/diagnosticOddsRatio.Rd man/drawAttritionDiagramPlp.Rd man/evaluateMultiplePlp.Rd man/evaluatePlp.Rd man/externalValidatePlp.Rd man/f1Score.Rd man/falseDiscoveryRate.Rd man/falseNegativeRate.Rd man/falseOmissionRate.Rd man/falsePositiveRate.Rd man/fitGLMModel.Rd man/fitPlp.Rd man/getAttritionTable.Rd man/getCalibration.Rd man/getPlpData.Rd man/getPlpTable.Rd man/getPredictionDistribution.Rd man/getThresholdSummary.Rd man/interpretInstallCode.Rd man/launchDiagnosticsExplorer.Rd man/listAppend.Rd man/loadEnsemblePlpModel.Rd man/loadEnsemblePlpResult.Rd man/loadPlpData.Rd man/loadPlpFromCsv.Rd man/loadPlpModel.Rd man/loadPlpResult.Rd man/loadPrediction.Rd man/loadPredictionAnalysisList.Rd man/negativeLikelihoodRatio.Rd man/negativePredictiveValue.Rd man/outcomeSurvivalPlot.Rd man/personSplitter.Rd man/plotDemographicSummary.Rd man/plotF1Measure.Rd man/plotGeneralizability.Rd man/plotLearningCurve.Rd man/plotPlp.Rd man/plotPrecisionRecall.Rd man/plotPredictedPDF.Rd man/plotPredictionDistribution.Rd man/plotPreferencePDF.Rd man/plotRoc.Rd man/plotSmoothCalibration.Rd man/plotSparseCalibration.Rd man/plotSparseCalibration2.Rd man/plotSparseRoc.Rd man/plotVariableScatterplot.Rd man/plpDataSimulationProfile.Rd man/positiveLikelihoodRatio.Rd man/positivePredictiveValue.Rd man/predictAndromeda.Rd man/predictPlp.Rd man/predictProbabilities.Rd man/randomSplitter.Rd man/registerParallelBackend.Rd man/registerSequentialBackend.Rd man/runEnsembleModel.Rd man/runPlp.Rd man/runPlpAnalyses.Rd man/saveEnsemblePlpModel.Rd man/saveEnsemblePlpResult.Rd man/savePlpData.Rd man/savePlpModel.Rd man/savePlpResult.Rd man/savePlpToCsv.Rd man/savePrediction.Rd man/savePredictionAnalysisList.Rd man/sensitivity.Rd man/setAdaBoost.Rd man/setCIReNN.Rd man/setCNNTorch.Rd man/setCovNN.Rd man/setCovNN2.Rd man/setCoxModel.Rd man/setDecisionTree.Rd man/setDeepNN.Rd man/setGBMSurvival.Rd man/setGradientBoostingMachine.Rd man/setKNN.Rd man/setLRTorch.Rd man/setLassoLogisticRegression.Rd man/setMLP.Rd man/setMLPTorch.Rd man/setNaiveBayes.Rd man/setPythonEnvironment.Rd man/setRNNTorch.Rd man/setRandomForest.Rd man/setRandomForestQuantileRegressor.Rd man/setSVM.Rd man/setSagemakerBinary.Rd man/similarPlpData.Rd man/simulatePlpData.Rd man/specificity.Rd man/subjectSplitter.Rd man/timeSplitter.Rd man/toSparseM.Rd man/toSparseTorchPython.Rd man/transferLearning.Rd man/transportModel.Rd man/transportPlp.Rd man/viewMultiplePlp.Rd man/viewPlp.Rd

src/Auc.cpp

src/Auc.h

src/ByMax.cpp

src/ByMax.h

src/BySum.cpp

src/BySum.h

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/RcppWrapper.cpp

tests/testthat.R tests/testthat/helper-objects.R tests/testthat/test-andromedahelperfunctions.R tests/testthat/test-apply.R tests/testthat/test-attrition.R tests/testthat/test-dataSplitting.R tests/testthat/test-diagnostic.R tests/testthat/test-document.R tests/testthat/test-ensemble.R tests/testthat/test-evaluation.R tests/testthat/test-fitting.R tests/testthat/test-formatting.R tests/testthat/test-helperfunctions.R tests/testthat/test-importexport.R tests/testthat/test-keras.R tests/testthat/test-learningCurves.R tests/testthat/test-multiplePlp.R tests/testthat/test-paramchecks.R tests/testthat/test-plotting.R tests/testthat/test-population.R tests/testthat/test-prediction.R tests/testthat/test-saveloadplp.R tests/testthat/test-shiny.R tests/testthat/test-survival.R tests/testthat/test-torch.R tests/testthat/test-validation.R vignettes/AddingCustomAlgorithms.Rmd vignettes/BuildingDeepLearningModels.Rmd vignettes/BuildingEnsembleModels.Rmd vignettes/BuildingMultiplePredictiveModels.Rmd vignettes/BuildingPredictiveModels.Rmd

vignettes/CovCNN.png

vignettes/CreatingLearningCurves.Rmd vignettes/CreatingNetworkStudies.Rmd vignettes/CreatingShinyApp.Rmd

vignettes/Diagram.png

vignettes/Figure1.png

vignettes/InstallationGuide.Rmd vignettes/PatientLevelPrediction.rmd

vignettes/PatientLevelPredictionFigures.pptx

vignettes/Videos.rmd

vignettes/arch1.png

vignettes/atlasdownload1.png

vignettes/atlasdownload2.png

vignettes/atlasplp1.png

vignettes/atlasplp2.png

vignettes/atlasplp3.png

vignettes/atlasplp4.png

vignettes/atlasplp5.png

vignettes/cirenn.png

vignettes/cnn_lstm.png

vignettes/cnn_mlf2.png

vignettes/conv_arch1.png

vignettes/conv_arch2.png

vignettes/covcnn2.png

vignettes/demographicSummary.png

vignettes/ensemble.png

vignettes/example1/ATLAS_O.PNG

vignettes/example1/ATLAS_T.PNG

vignettes/example2/aceinhibitors.png

vignettes/example2/angioedema.png

vignettes/f1Measure.png

vignettes/f1score.png

vignettes/generalizability.png

vignettes/learningCurve.png

vignettes/learningCurveBias.png

vignettes/learningCurvePlot.png

vignettes/learningCurveVariance.png

vignettes/lstm_last.png

vignettes/popdef1.png

vignettes/popdef2.png

vignettes/popdef3.png

vignettes/popdef4.png

vignettes/popdef5.png

vignettes/popdef6.png

vignettes/preamble.tex

vignettes/precisionRecall.png

vignettes/predictedPDF.png

vignettes/predictionDistribution.png

vignettes/preferencePDF.png

vignettes/problems.png

vignettes/shinyroc.PNG

vignettes/shinysummary.PNG

vignettes/smoothCalibration.jpeg

vignettes/sparseCalibration.png

vignettes/sparseROC.png

vignettes/studydesign.png

vignettes/variableScatterplot.png

hxia/plp-git-demo documentation built on March 19, 2021, 1:54 a.m.