Files in OHDSI/PatientLevelPrediction

Developing patient level prediction using data in the OMOP Common Data Model

.Rbuildignore

.cproject

.gitattributes

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/R_CMD_check_Hades.yaml

.github/workflows/R_CMD_check_main_weekly.yaml

.github/workflows/nightly_cleanup_Hades.yml

.github/workflows/pkgdown.yaml

.gitignore

.project

.settings/org.eclipse.cdt.managedbuilder.core.prefs

DESCRIPTION

NAMESPACE

NEWS.md

PatientLevelPrediction.Rproj

R/AdditionalCovariates.R R/AndromedaHelperFunctions.R R/CalibrationSummary.R R/CovariateSummary.R R/CyclopsModels.R R/CyclopsSettings.R R/DataSplitting.R R/DatabaseMigration.R R/DemographicSummary.R R/DiagnosePlp.R R/EvaluatePlp.R R/EvaluationSummary.R R/ExternalValidatePlp.R R/ExtractData.R R/FeatureEngineering.R R/FeatureImportance.R R/Fit.R R/Formatting.R R/GradientBoostingMachine.R R/HelperFunctions.R R/ImportFromCsv.R R/KNN.R R/LearningCurve.R R/LightGBM.R R/Logging.R R/ParamChecks.R R/PatientLevelPrediction.R R/Plotting.R R/PopulationSettings.R R/Predict.R R/PredictionDistribution.R R/PreprocessingData.R R/RClassifier.R R/Recalibration.R R/RunMultiplePlp.R R/RunPlp.R R/RunPlpHelpers.R R/Sampling.R R/SaveLoadPlp.R R/Simulation.R R/SklearnClassifier.R R/SklearnClassifierHelpers.R R/SklearnClassifierSettings.R R/SklearnToJson.R R/ThresholdSummary.R R/ViewShinyPlp.R R/uploadToDatabase.R R/uploadToDatabaseDiagnostics.R R/uploadToDatabaseModelDesign.R R/uploadToDatabasePerformance.R README.md

_pkgdown.yml

compare_versions

data/plpDataSimulationProfile.rda

demo/00Index

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

deploy.sh

extras/PackageMaintenance.R extras/VignetteDataFetch.R extras/checkPlpInstallation.R extras/convertOldRunPlp.R extras/old-RandomForestQuantileRegressor.R extras/old-SageMakerBinary.R extras/old-modelAsCovariate.R extras/testAllClassifiers.R

inst/CITATION

inst/doc/AddingCustomFeatureEngineering.pdf inst/doc/AddingCustomModels.pdf inst/doc/AddingCustomSamples.pdf inst/doc/AddingCustomSplitting.pdf inst/doc/BuildingMultiplePredictiveModels.pdf inst/doc/BuildingPredictiveModels.pdf inst/doc/CreatingLearningCurves.pdf inst/doc/CreatingNetworkstudies.pdf inst/doc/CreatingShinyApp.pdf inst/doc/InstallationGuide.pdf

inst/settings/resultsDataModelSpecification.csv

inst/shinyConfig.json

inst/shinyConfigUpdate.json

inst/sql/postgresql/Migration_1-store_version.sql

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/PlpResultTables.sql

inst/sql/sql_server/RemoveCohortTempTables.sql

inst/sql/sql_server/UpdateVersionNumber.sql

inst/sql/sql_server/migrations/Migration_1-store_version.sql

inst/sql/sqlite/PlpResultTables.sql

inst/sql/sqlite/migrations/Migration_1-store_version.sql

man/MapIds.Rd man/PatientLevelPrediction.Rd man/accuracy.Rd man/addDiagnosePlpToDatabase.Rd man/addMultipleDiagnosePlpToDatabase.Rd man/addMultipleRunPlpToDatabase.Rd man/addRunPlpToDatabase.Rd man/averagePrecision.Rd man/brierScore.Rd man/calibrationLine.Rd man/computeAuc.Rd man/computeGridPerformance.Rd man/configurePython.Rd man/covariateSummary.Rd man/createCohortCovariateSettings.Rd man/createDatabaseDetails.Rd man/createDatabaseList.Rd man/createDatabaseSchemaSettings.Rd man/createDefaultExecuteSettings.Rd man/createDefaultSplitSetting.Rd man/createExecuteSettings.Rd man/createFeatureEngineeringSettings.Rd man/createLearningCurve.Rd man/createLogSettings.Rd man/createModelDesign.Rd man/createPlpResultTables.Rd man/createPreprocessSettings.Rd man/createRandomForestFeatureSelection.Rd man/createRestrictPlpDataSettings.Rd man/createSampleSettings.Rd man/createSplineSettings.Rd man/createStratifiedImputationSettings.Rd man/createStudyPopulation.Rd man/createStudyPopulationSettings.Rd man/createTempModelLoc.Rd man/createUnivariateFeatureSelection.Rd man/createValidationSettings.Rd man/diagnoseMultiplePlp.Rd man/diagnosePlp.Rd man/diagnosticOddsRatio.Rd man/evaluatePlp.Rd man/externalValidateDbPlp.Rd man/extractDatabaseToCsv.Rd man/f1Score.Rd man/falseDiscoveryRate.Rd man/falseNegativeRate.Rd man/falseOmissionRate.Rd man/falsePositiveRate.Rd man/fitPlp.Rd man/getCalibrationSummary.Rd man/getCohortCovariateData.Rd man/getDemographicSummary.Rd man/getPlpData.Rd man/getPredictionDistribution.Rd man/getPredictionDistribution_binary.Rd man/getThresholdSummary.Rd man/getThresholdSummary_binary.Rd man/ici.Rd man/insertCsvToDatabase.Rd man/insertModelDesignInDatabase.Rd man/insertResultsToSqlite.Rd man/listAppend.Rd man/listCartesian.Rd man/loadPlpAnalysesJson.Rd man/loadPlpData.Rd man/loadPlpModel.Rd man/loadPlpResult.Rd man/loadPlpShareable.Rd man/loadPrediction.Rd man/migrateDataModel.Rd man/modelBasedConcordance.Rd man/negativeLikelihoodRatio.Rd man/negativePredictiveValue.Rd man/outcomeSurvivalPlot.Rd man/pfi.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/plotSmoothCalibration.Rd man/plotSparseCalibration.Rd man/plotSparseCalibration2.Rd man/plotSparseRoc.Rd man/plotVariableScatterplot.Rd man/plpDataSimulationProfile.Rd man/positiveLikelihoodRatio.Rd man/positivePredictiveValue.Rd man/predictCyclops.Rd man/predictPlp.Rd man/preprocessData.Rd man/recalibratePlp.Rd man/recalibratePlpRefit.Rd man/runMultiplePlp.Rd man/runPlp.Rd man/savePlpAnalysesJson.Rd man/savePlpData.Rd man/savePlpModel.Rd man/savePlpResult.Rd man/savePlpShareable.Rd man/savePrediction.Rd man/sensitivity.Rd man/setAdaBoost.Rd man/setCoxModel.Rd man/setDecisionTree.Rd man/setGradientBoostingMachine.Rd man/setIterativeHardThresholding.Rd man/setKNN.Rd man/setLassoLogisticRegression.Rd man/setLightGBM.Rd man/setMLP.Rd man/setNaiveBayes.Rd man/setPythonEnvironment.Rd man/setRandomForest.Rd man/setSVM.Rd man/simulatePlpData.Rd man/sklearnFromJson.Rd man/sklearnToJson.Rd man/specificity.Rd man/splitData.Rd man/toSparseM.Rd man/validateMultiplePlp.Rd man/viewDatabaseResultPlp.Rd man/viewMultiplePlp.Rd man/viewPlp.Rd tests/testthat.R tests/testthat/helper-expectations.R tests/testthat/helper-functions.R tests/testthat/helper-objects.R tests/testthat/test-KNN.R tests/testthat/test-LightGBM.R tests/testthat/test-PredictionDistribution.R tests/testthat/test-ThresholdSummary.R tests/testthat/test-UploadToDatabase.R tests/testthat/test-andromedahelperfunctions.R tests/testthat/test-covariateExtras.R tests/testthat/test-covariateSummary.R tests/testthat/test-cyclopsModels.R tests/testthat/test-dataSplitting.R tests/testthat/test-demographicSummary.R tests/testthat/test-diagnostic.R tests/testthat/test-evaluation.R tests/testthat/test-extractData.R tests/testthat/test-featureEngineering.R tests/testthat/test-featureImportance.R tests/testthat/test-fitting.R tests/testthat/test-formatting.R tests/testthat/test-getCalibration.R tests/testthat/test-helperfunctions.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-preprocessingData.R tests/testthat/test-rclassifier.R tests/testthat/test-recalibration.R tests/testthat/test-runPlpHelpers.R tests/testthat/test-sampling.R tests/testthat/test-saveloadplp.R tests/testthat/test-sklearnClassifier.R tests/testthat/test-sklearnClassifierHelpers.R tests/testthat/test-sklearnClassifierSettings.R tests/testthat/test-sklearnJson.R tests/testthat/test-validation.R

vignettes/.gitignore

vignettes/AddingCustomFeatureEngineering.Rmd vignettes/AddingCustomModels.Rmd vignettes/AddingCustomSamples.Rmd vignettes/AddingCustomSplitting.Rmd vignettes/BenchmarkTasks.Rmd vignettes/BestPractices.rmd vignettes/BuildingMultiplePredictiveModels.Rmd vignettes/BuildingPredictiveModels.Rmd vignettes/ConstrainedPredictors.Rmd vignettes/CreatingLearningCurves.Rmd

vignettes/CreatingLearningCurves.nb.html

vignettes/CreatingNetworkStudies.Rmd

vignettes/Diagram.png

vignettes/Figure1.png

vignettes/InstallationGuide.Rmd

vignettes/PLPv5.0.0.html

vignettes/PatientLevelPredictionFigures.pptx

vignettes/Videos.rmd

vignettes/atlasdownload1.png

vignettes/atlasdownload2.png

vignettes/atlasplp1.png

vignettes/atlasplp2.png

vignettes/atlasplp3.png

vignettes/atlasplp4.png

vignettes/atlasplp5.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/plpDiagram.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 April 6, 2024, 11:50 p.m.