applyEnsembleModel: Apply trained ensemble model on new data Apply a Patient...

In hxia/plp-git-demo: Package for patient level prediction using data in the OMOP Common Data Model

Description

Apply trained ensemble model on new data Apply a Patient Level Prediction model on Patient Level Prediction Data and get the predicted risk in [0,1] for each person in the population. If the user inputs a population with an outcomeCount column then the function also returns the evaluation of the prediction (AUC, brier score, calibration)

Usage

applyEnsembleModel(
  population,
  dataList,
  ensembleModel,
  analysisId = NULL,
  calculatePerformance = T
)

Arguments

population	The population of people who you want to predict the risk for
dataList	The plpData list for the population
ensembleModel	The trained ensemble model returned by running runEnsembleModel
analysisId	The analysis ID, which is the ID of running ensemble model training.
calculatePerformance	Whether to also calculate the performance metrics [default TRUE]

Examples

## Not run: 
# load the model and data
plpData <- loadPlpData("plpdata/")
results <- PatientLevelPrediction::runEnsembleModel(population,
                                                    dataList = list(plpData, plpData),
                                                    modelList = list(model, model),
                                                    testSplit = "person",
                                                    testFraction = 0.2,
                                                    nfold = 3,
                                                    splitSeed = 1000,
                                                    ensembleStrategy = "stacked")
# use the same population settings as the model:
populationSettings <- plpModel$populationSettings
populationSettings$plpData <- plpData
population <- do.call(createStudyPopulation, populationSettings)

# get the prediction, please make sure the ensemble strategy for training and apply is the same:
prediction <- applyEnsembleModel(population,
                                 dataList = list(plpData, plpData),
                                 ensembleModel = results,
                                 analysisId = NULL)$prediction

## End(Not run)

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