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

accuracyCalculate the accuracy
applyEnsembleModelApply trained ensemble model on new data Apply a Patient...
applyModelApply train model on new data Apply a Patient Level...
averagePrecisionCalculate the average precision
brierScorebrierScore
bySumFfCompute sum of values binned by a second variable
calibrationLinecalibrationLine
checkPlpInstallationCheck PatientLevelPrediction and its dependencies are...
clearffTempDirclearffTempDir
combinePlpModelSettingscombine two objects specifying multiple Plp model settings
computeAucCompute the area under the ROC curve
computeAucFromDataFramesCompute the area under the ROC curve
createCohortcreateCohort - Loads all the cohort sql in a network study...
createExistingModelSqlApply an existing logistic regression prediction model
createLearningCurvecreateLearningCurve
createLearningCurveParcreateLearningCurvePar
createLrSqlConvert logistic regression model to sql code...
createPlpJournalDocumentcreatePlpJournalDocument
createPlpModelSettingscreate a an object specifying the multiple Plp model settings
createPlpReportcreatePlpReport
createStudyPopulationCreate a study population
createStudyPopulationSettingscreate the study population settings
diagnosticOddsRatioCalculate the diagnostic odds ratio
drawAttritionDiagramPlpDraw the attrition diagram
evaluateExistingModelevaluateExistingModel
evaluateMultiplePlpexternally validate the multiple plp models across new...
evaluatePlpevaluatePlp
exportPlpDataToCsvExport all data in a plpData object to CSV files
exportPlpResultexportPlpResult exports an object returned by runPlp into a...
externalValidatePlpexternalValidatePlp - Validate a model on new databases
f1ScoreCalculate the f1Score
falseDiscoveryRateCalculate the falseDiscoveryRate
falseNegativeRateCalculate the falseNegativeRate
falseOmissionRateCalculate the falseOmissionRate
falsePositiveRateCalculate the falsePositiveRate
fitGLMModelFit a predictive model
fitPlpfitPlp
getAttritionTableGet the attrition table for a population
getCalibrationGet a sparse summary of the calibration
getCovariateDataGet the covaridate data for a cohort table
getModelDetailsGet the predictive model details
getPlpDataGet the patient level prediction data from the server
getPlpTableCreate a dataframe with the summary details of the population...
getPredictionDistributionCalculates the prediction distribution
getThresholdSummaryCalculate all measures for sparse ROC
grepCovariateNamesExtract covariate names
insertDbPopulationInsert a population into a database
interpretInstallCodeTells you the package issue
loadEnsemblePlpModelloads the Ensmeble plp model and return a model list
loadEnsemblePlpResultloads the Ensemble plp results
loadPlpDataLoad the cohort data from a folder
loadPlpModelloads the plp model
loadPlpResultLoads the evalaution dataframe
loadPredictionLoads the prediciton dataframe to csv
loadPredictionAnalysisListLoad the multiple prediction json settings from a file
negativeLikelihoodRatioCalculate the negativeLikelihoodRatio
negativePredictiveValueCalculate the negativePredictiveValue
packageResultsPackage the results for sharing with OHDSI researchers
PatientLevelPredictionPatientLevelPrediction
personSplitterSplit data into random subsets stratified by class
plotDemographicSummaryPlot the Observed vs. expected incidence, by age and gender
plotF1MeasurePlot the F1 measure efficiency frontier using the sparse...
plotGeneralizabilityPlot the train/test generalizability diagnostic
plotLearningCurveplotLearningCurve
plotPlpPlot all the PatientLevelPrediction plots
plotPrecisionRecallPlot the precision-recall curve using the sparse...
plotPredictedPDFPlot the Predicted probability density function, showing...
plotPredictionDistributionPlot the side-by-side boxplots of prediction distribution, by...
plotPreferencePDFPlot the preference score probability density function,...
plotRocPlot the ROC curve
plotSmoothCalibrationPlot the smooth calibration as detailed in Calster et al. "A...
plotSparseCalibrationPlot the calibration
plotSparseCalibration2Plot the conventional calibration
plotSparseRocPlot the ROC curve using the sparse thresholdSummary data...
plotVariableScatterplotPlot the variable importance scatterplot
plpDataSimulationProfileA simulation profile
positiveLikelihoodRatioCalculate the positiveLikelihoodRatio
positivePredictiveValueCalculate the positivePredictiveValue
predictFfdfGenerated predictions from a regression model
predictPlppredictPlp
predictProbabilitiesCreate predictive probabilities
registerParallelBackendregisterParallelBackend
registerSequentialBackendregisterSequentialBackend
runEnsembleModelensemble - Create an ensembling model using different models
runPlprunPlp - Train and evaluate the model
runPlpAnalysesRun a list of predictions
saveEnsemblePlpModelsaves the Ensmeble plp model
saveEnsemblePlpResultsaves the Ensemble plp results
savePlpDataSave the cohort data to folder
savePlpModelSaves the plp model
savePlpResultSaves the result from runPlp into the location directory
savePredictionSaves the prediction dataframe to csv
sensitivityCalculate the sensitivity
setAdaBoostCreate setting for AdaBoost with python
setCIReNNCreate setting for CIReNN model
setCNNTorchCreate setting for CNN model with python
setCovNNCreate setting for multi-resolution CovNN model (stucture...
setCovNN2Create setting for CovNN2 model - convolution across input...
setDecisionTreeCreate setting for DecisionTree with python
setDeepNNCreate setting for DeepNN model
setGradientBoostingMachineCreate setting for gradient boosting machine model using...
setKNNCreate setting for knn model
setLassoLogisticRegressionCreate setting for lasso logistic regression
setLRTorchCreate setting for logistics regression model with python
setMLPCreate setting for neural network model with python
setMLPTorchCreate setting for neural network model with python
setNaiveBayesCreate setting for naive bayes model with python
setRandomForestCreate setting for random forest model with python (very...
setRNNTorchCreate setting for RNN model with python
similarPlpDataExtract new plpData using plpModel settings use metadata in...
simulatePlpDataGenerate simulated data
specificityCalculate the specificity
standardOutputstandardOutput - takes the output of runPlp or evaluatePlp...
submitResultssubmitResults - sends a zipped folder to the OHDSI network...
timeSplitterSplit test/train data by time and then partitions training...
toPlpDataConvert matrix into plpData
toSparseMConvert the plpData in COO format into a sparse R matrix
toSparsePythonConvert the plpData in COO format into a sparse python matrix
toSparseTorchPythonConvert the plpData in COO format into a sparse python matrix...
transportModelTransports a plpModel to a new location and removes sensitive...
transportPlpTransports a plpResult to a new location and removed...
viewPlpviewPlp - Interactively view the performance and model...
OHDSI/PatientLevelPrediction documentation built on Sept. 9, 2018, 3:40 a.m.