Files in OHDSI/PatientLevelPrediction
Package for patient level prediction using data in the OMOP Common Data Model

.Rbuildignore
.cproject
.gitattributes
.gitignore
.project
.settings/org.eclipse.cdt.managedbuilder.core.prefs
.travis.yml
DESCRIPTION
NAMESPACE
PatientLevelPrediction.Rproj
R/AdaBoost.R R/ApplyPlp.R R/AttritionDiagramPlp.R R/CIReNN.R R/CNNTorch.R R/CovNN.R R/CovNN2.R R/CreatePlpDocument.R R/DataSplitting.R R/DecisionTree.R R/DeepNN.R R/Ensemble.R R/EvaluatePlp.R R/ExternalValidatePlp.R R/FfHelperFunctions.R R/Fit.R R/FitGLMModel.R R/Formatting.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/PackagePlp.R R/Parallel.R R/ParamChecks.R R/PatientLevelPrediction.R R/Plotting.R R/Predict.R R/RNNTorch.R R/RandomForest.R R/RcppExports.R R/RunMultiplePlp.R R/RunPlp.R R/SaveLoadPlp.R R/Simulation.R R/StudyPopulation.R R/ViewMultiplePlp.R R/ViewPlp.R README.md
compare_versions
data/plpDataSimulationProfile.rda
demo/00Index
demo/EnsembleModelDemo.R demo/LearningCurveDemo.R demo/SingleModelDemo.R
deploy.sh
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/BuildingDeepLearningModels.pdf inst/doc/BuildingEnsembleModels.pdf inst/doc/BuildingMultiplePredictiveModels.pdf inst/doc/BuildingPredictiveModels.pdf inst/doc/CreatingNetworkstudies.pdf
inst/doc/Figure1.png
inst/doc/GeneratingLearningCurves.pdf inst/doc/ImplementingExistingModels.pdf inst/doc/InstallationGuide.pdf
inst/doc/patientLevelPredictionRun.csv
inst/python/TorchUtils.py
inst/python/adaBoost.py
inst/python/decisionTree.py
inst/python/deepTorch.py
inst/python/finalRandomForest.py
inst/python/mlp.py
inst/python/naive_bayes.py
inst/python/python_predict.py
inst/python/randomForestCV.py
inst/python/rf_var_imp.py
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/bySumFf.Rd man/calibrationLine.Rd man/checkPlpInstallation.Rd man/checkffFolder.Rd man/clearffTempDir.Rd man/combinePlpModelSettings.Rd man/computeAuc.Rd man/computeAucFromDataFrames.Rd man/createCohort.Rd man/createExistingModelSql.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/diagnosticOddsRatio.Rd man/drawAttritionDiagramPlp.Rd man/evaluateExistingModel.Rd man/evaluateMultiplePlp.Rd man/evaluatePlp.Rd man/exportPlpDataToCsv.Rd man/exportPlpResult.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/getCovariateData.Rd man/getModelDetails.Rd man/getPlpData.Rd man/getPlpTable.Rd man/getPredictionDistribution.Rd man/getThresholdSummary.Rd man/grepCovariateNames.Rd man/insertDbPopulation.Rd man/interpretInstallCode.Rd man/loadEnsemblePlpModel.Rd man/loadEnsemblePlpResult.Rd man/loadPlpData.Rd man/loadPlpModel.Rd man/loadPlpResult.Rd man/loadPrediction.Rd man/loadPredictionAnalysisList.Rd man/negativeLikelihoodRatio.Rd man/negativePredictiveValue.Rd man/packageResults.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/predictFfdf.Rd man/predictPlp.Rd man/predictProbabilities.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/savePrediction.Rd man/savePredictionAnalysisList.Rd man/sensitivity.Rd man/setAdaBoost.Rd man/setCIReNN.Rd man/setCNNTorch.Rd man/setCovNN.Rd man/setCovNN2.Rd man/setDecisionTree.Rd man/setDeepNN.Rd man/setGradientBoostingMachine.Rd man/setKNN.Rd man/setLRTorch.Rd man/setLassoLogisticRegression.Rd man/setMLP.Rd man/setMLPTorch.Rd man/setNaiveBayes.Rd man/setRNNTorch.Rd man/setRandomForest.Rd man/similarPlpData.Rd man/simulatePlpData.Rd man/specificity.Rd man/standardOutput.Rd man/submitResults.Rd man/timeSplitter.Rd man/toPlpData.Rd man/toSparseM.Rd man/toSparsePython.Rd man/toSparseTorchPython.Rd man/transportModel.Rd man/transportPlp.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/test-dataSplitting.R tests/testthat/test-document.R tests/testthat/test-evaluation.R tests/testthat/test-formatting.R tests/testthat/test-multiplePlp.R tests/testthat/test-package.R tests/testthat/test-plotting.R tests/testthat/test-population.R tests/testthat/test-prediction.R tests/testthat/test-transport.R tests/testthat/test-validation.R
vignettes/ATLAS_O.PNG
vignettes/ATLAS_T.PNG
vignettes/AddingCustomAlgorithms.Rmd vignettes/AddingExistingModels.Rmd vignettes/BuildingDeepLearningModels.Rmd vignettes/BuildingEnsembleModels.Rmd vignettes/BuildingMultiplePredictiveModels.Rmd vignettes/BuildingPredictiveModels.Rmd
vignettes/CovCNN.png
vignettes/CreatingNetworkStudies.Rmd vignettes/CustomPredictionAlgorithms.Rmd
vignettes/Diagram.png
vignettes/Figure1.png
vignettes/GeneratingLearningCurves.Rmd vignettes/ImplementingExistingModels.Rmd vignettes/InstallationGuide.Rmd
vignettes/PatientLevelPredictionFigures.pptx
vignettes/PlottingLearningCurves.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/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
OHDSI/PatientLevelPrediction documentation built on Oct. 14, 2018, 6:11 p.m.