{
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  "Title": "Develop Clinical Prediction Models Using the Common Data Model",
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  "Date": "2026-03-09",
  "Authors@R": "c(\nperson(\"Egill\", \"Fridgeirsson\", email = \"e.fridgeirsson@erasmusmc.nl\", role = c(\"aut\", \"cre\")),\nperson(\"Jenna\", \"Reps\", email = \"jreps@its.jnj.com\", role = c(\"aut\")),\nperson(\"Martijn\", \"Schuemie\", role = c(\"aut\")),\nperson(\"Marc\", \"Suchard\", role = c(\"aut\")),\nperson(\"Patrick\", \"Ryan\", role = c(\"aut\")),\nperson(\"Peter\", \"Rijnbeek\", role = c(\"aut\")),\nperson(\"Observational Health Data Science and Informatics\", role = c(\"cph\")))",
  "Description": "A user friendly way to create patient level prediction\nmodels using the Observational Medical Outcomes Partnership\nCommon Data Model. Given a cohort of interest and an outcome of\ninterest, the package can use data in the Common Data Model to\nbuild a large set of features. These features can then be used\nto fit a predictive model with a number of machine learning\nalgorithms. This is further described in Reps (2017)\n<doi:10.1093/jamia/ocy032>.",
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    "createRestrictPlpDataSettings",
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    "createStudyPopulation",
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    "createTuningMetric",
    "createUnivariateFeatureSelection",
    "createValidationDesign",
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    "getDemographicSummary",
    "getEunomiaPlpData",
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    "insertCsvToDatabase",
    "insertResultsToSqlite",
    "listAppend",
    "listCartesian",
    "loadPlpAnalysesJson",
    "loadPlpData",
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    "loadPlpResult",
    "loadPlpShareable",
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    "MapIds",
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    "pfi",
    "plotDemographicSummary",
    "plotF1Measure",
    "plotGeneralizability",
    "plotLearningCurve",
    "plotNetBenefit",
    "plotPlp",
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    "plotPredictedPDF",
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    "runMultiplePlp",
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      "page": "averagePrecision",
      "title": "Calculate the average precision",
      "topics": [
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      ]
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      "topics": [
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      "title": "calibrationLine",
      "topics": [
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    {
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      "title": "Compute the area under the ROC curve",
      "topics": [
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      ]
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    {
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      "title": "Compute the area under the Precision-Recall curve",
      "topics": [
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    },
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      "title": "Computes grid performance for a hyperparameter combination (backwards compatible)",
      "topics": [
        "computeGridPerformance"
      ]
    },
    {
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      "title": "Sets up a python environment to use for PLP (can be conda or venv)",
      "topics": [
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      ]
    },
    {
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      "title": "covariateSummary",
      "topics": [
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    },
    {
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      "title": "Extracts covariates based on cohorts",
      "topics": [
        "createCohortCovariateSettings"
      ]
    },
    {
      "page": "createDatabaseDetails",
      "title": "Create a setting that holds the details about the cdmDatabase connection for data extraction",
      "topics": [
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      ]
    },
    {
      "page": "createDatabaseSchemaSettings",
      "title": "Create the PatientLevelPrediction database result schema settings",
      "topics": [
        "createDatabaseSchemaSettings"
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    },
    {
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      "title": "Creates default list of settings specifying what parts of runPlp to execute",
      "topics": [
        "createDefaultExecuteSettings"
      ]
    },
    {
      "page": "createDefaultSplitSetting",
      "title": "Create the settings for defining how the plpData are split into test/validation/train sets using default splitting functions (either random stratified by outcome, time or subject splitting)",
      "topics": [
        "createDefaultSplitSetting"
      ]
    },
    {
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      "title": "Creates list of settings specifying what parts of runPlp to execute",
      "topics": [
        "createExecuteSettings"
      ]
    },
    {
      "page": "createExistingSplitSettings",
      "title": "Create the settings for defining how the plpData are split into test/validation/train sets using an existing split - good to use for reproducing results from a different run",
      "topics": [
        "createExistingSplitSettings"
      ]
    },
    {
      "page": "createFeatureEngineeringSettings",
      "title": "Create the settings for defining any feature engineering that will be done",
      "topics": [
        "createFeatureEngineeringSettings"
      ]
    },
    {
      "page": "createGlmModel",
      "title": "createGlmModel",
      "topics": [
        "createGlmModel"
      ]
    },
    {
      "page": "createHyperparameterSettings",
      "title": "Create Hyperparameter Settings",
      "topics": [
        "createHyperparameterSettings"
      ]
    },
    {
      "page": "createIterativeImputer",
      "title": "Create Iterative Imputer settings",
      "topics": [
        "createIterativeImputer"
      ]
    },
    {
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      "title": "createLearningCurve",
      "topics": [
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      ]
    },
    {
      "page": "createLogSettings",
      "title": "Create the settings for logging the progression of the analysis",
      "topics": [
        "createLogSettings"
      ]
    },
    {
      "page": "createModelDesign",
      "title": "Specify settings for developing a single model",
      "topics": [
        "createModelDesign"
      ]
    },
    {
      "page": "createNormalizer",
      "title": "Create the settings for normalizing the data @param type The type of normalization to use, either \"minmax\" or \"robust\"",
      "topics": [
        "createNormalizer"
      ]
    },
    {
      "page": "createPlpResultTables",
      "title": "Create the results tables to store PatientLevelPrediction models and results into a database",
      "topics": [
        "createPlpResultTables"
      ]
    },
    {
      "page": "createPreprocessSettings",
      "title": "Create the settings for preprocessing the trainData.",
      "topics": [
        "createPreprocessSettings"
      ]
    },
    {
      "page": "createRandomForestFeatureSelection",
      "title": "Create the settings for random foreat based feature selection",
      "topics": [
        "createRandomForestFeatureSelection"
      ]
    },
    {
      "page": "createRareFeatureRemover",
      "title": "Create the settings for removing rare features",
      "topics": [
        "createRareFeatureRemover"
      ]
    },
    {
      "page": "createRestrictPlpDataSettings",
      "title": "createRestrictPlpDataSettings define extra restriction settings when calling getPlpData",
      "topics": [
        "createRestrictPlpDataSettings"
      ]
    },
    {
      "page": "createSampleSettings",
      "title": "Create the settings for defining how the trainData from 'splitData' are sampled using default sample functions.",
      "topics": [
        "createSampleSettings"
      ]
    },
    {
      "page": "createSimpleImputer",
      "title": "Create Simple Imputer settings",
      "topics": [
        "createSimpleImputer"
      ]
    },
    {
      "page": "createSklearnIterativeImputer",
      "title": "Create scikit-learn Iterative Imputer settings",
      "topics": [
        "createSklearnIterativeImputer"
      ]
    },
    {
      "page": "createSklearnModel",
      "title": "Plug an existing scikit learn python model into the PLP framework",
      "topics": [
        "createSklearnModel"
      ]
    },
    {
      "page": "createSplineSettings",
      "title": "Create the settings for adding a spline for continuous variables",
      "topics": [
        "createSplineSettings"
      ]
    },
    {
      "page": "createStratifiedImputationSettings",
      "title": "Create the settings for using stratified imputation.",
      "topics": [
        "createStratifiedImputationSettings"
      ]
    },
    {
      "page": "createStudyPopulation",
      "title": "Create a study population",
      "topics": [
        "createStudyPopulation"
      ]
    },
    {
      "page": "createStudyPopulationSettings",
      "title": "create the study population settings",
      "topics": [
        "createStudyPopulationSettings"
      ]
    },
    {
      "page": "createTempModelLoc",
      "title": "Create a temporary model location",
      "topics": [
        "createTempModelLoc"
      ]
    },
    {
      "page": "createTuningMetric",
      "title": "Create a tuning metric descriptor",
      "topics": [
        "createTuningMetric"
      ]
    },
    {
      "page": "createUnivariateFeatureSelection",
      "title": "Create the settings for defining any feature selection that will be done",
      "topics": [
        "createUnivariateFeatureSelection"
      ]
    },
    {
      "page": "createValidationDesign",
      "title": "createValidationDesign - Define the validation design for external validation",
      "topics": [
        "createValidationDesign"
      ]
    },
    {
      "page": "createValidationSettings",
      "title": "createValidationSettings define optional settings for performing external validation",
      "topics": [
        "createValidationSettings"
      ]
    },
    {
      "page": "diagnoseMultiplePlp",
      "title": "Run a list of predictions diagnoses",
      "topics": [
        "diagnoseMultiplePlp"
      ]
    },
    {
      "page": "diagnosePlp",
      "title": "diagnostic - Investigates the prediction problem settings - use before training a model",
      "topics": [
        "diagnosePlp"
      ]
    },
    {
      "page": "evaluatePlp",
      "title": "evaluatePlp",
      "topics": [
        "evaluatePlp"
      ]
    },
    {
      "page": "externalValidateDbPlp",
      "title": "externalValidateDbPlp - Validate a model on new databases",
      "topics": [
        "externalValidateDbPlp"
      ]
    },
    {
      "page": "extractDatabaseToCsv",
      "title": "Exports all the results from a database into csv files",
      "topics": [
        "extractDatabaseToCsv"
      ]
    },
    {
      "page": "fitPlp",
      "title": "fitPlp",
      "topics": [
        "fitPlp"
      ]
    },
    {
      "page": "getCalibrationSummary",
      "title": "Get a sparse summary of the calibration",
      "topics": [
        "getCalibrationSummary"
      ]
    },
    {
      "page": "getCohortCovariateData",
      "title": "Extracts covariates based on cohorts",
      "topics": [
        "getCohortCovariateData"
      ]
    },
    {
      "page": "getDemographicSummary",
      "title": "Get a demographic summary",
      "topics": [
        "getDemographicSummary"
      ]
    },
    {
      "page": "getEunomiaPlpData",
      "title": "Create a plpData object from the Eunomia database'",
      "topics": [
        "getEunomiaPlpData"
      ]
    },
    {
      "page": "getPlpData",
      "title": "Extract the patient level prediction data from the server",
      "topics": [
        "getPlpData"
      ]
    },
    {
      "page": "getPredictionDistribution",
      "title": "Calculates the prediction distribution",
      "topics": [
        "getPredictionDistribution"
      ]
    },
    {
      "page": "getThresholdSummary",
      "title": "Calculate all measures for sparse ROC",
      "topics": [
        "getThresholdSummary"
      ]
    },
    {
      "page": "ici",
      "title": "Calculate the Integrated Calibration Index from Austin and Steyerberg https://onlinelibrary.wiley.com/doi/full/10.1002/sim.8281",
      "topics": [
        "ici"
      ]
    },
    {
      "page": "insertCsvToDatabase",
      "title": "Function to insert results into a database from csvs",
      "topics": [
        "insertCsvToDatabase"
      ]
    },
    {
      "page": "insertResultsToSqlite",
      "title": "Create sqlite database with the results",
      "topics": [
        "insertResultsToSqlite"
      ]
    },
    {
      "page": "listAppend",
      "title": "join two lists",
      "topics": [
        "listAppend"
      ]
    },
    {
      "page": "listCartesian",
      "title": "Cartesian product",
      "topics": [
        "listCartesian"
      ]
    },
    {
      "page": "loadPlpAnalysesJson",
      "title": "Load the multiple prediction json settings from a file",
      "topics": [
        "loadPlpAnalysesJson"
      ]
    },
    {
      "page": "loadPlpData",
      "title": "Load the plpData from a folder",
      "topics": [
        "loadPlpData"
      ]
    },
    {
      "page": "loadPlpModel",
      "title": "loads the plp model",
      "topics": [
        "loadPlpModel"
      ]
    },
    {
      "page": "loadPlpResult",
      "title": "Loads the evalaution dataframe",
      "topics": [
        "loadPlpResult"
      ]
    },
    {
      "page": "loadPlpShareable",
      "title": "Loads the plp result saved as json/csv files for transparent sharing",
      "topics": [
        "loadPlpShareable"
      ]
    },
    {
      "page": "loadPrediction",
      "title": "Loads the prediction dataframe to json",
      "topics": [
        "loadPrediction"
      ]
    },
    {
      "page": "MapIds",
      "title": "Map covariate and row Ids so they start from 1",
      "topics": [
        "MapIds"
      ]
    },
    {
      "page": "migrateDataModel",
      "title": "Migrate Data model",
      "topics": [
        "migrateDataModel"
      ]
    },
    {
      "page": "modelBasedConcordance",
      "title": "Calculate the model-based concordance, which is a calculation of the expected discrimination performance of a model under the assumption the model predicts the \"TRUE\" outcome as detailed in van Klaveren et al. https://pubmed.ncbi.nlm.nih.gov/27251001/",
      "topics": [
        "modelBasedConcordance"
      ]
    },
    {
      "page": "outcomeSurvivalPlot",
      "title": "Plot the outcome incidence over time",
      "topics": [
        "outcomeSurvivalPlot"
      ]
    },
    {
      "page": "pfi",
      "title": "Permutation Feature Importance",
      "topics": [
        "pfi"
      ]
    },
    {
      "page": "plotDemographicSummary",
      "title": "Plot the Observed vs. expected incidence, by age and gender",
      "topics": [
        "plotDemographicSummary"
      ]
    },
    {
      "page": "plotF1Measure",
      "title": "Plot the F1 measure efficiency frontier using the sparse thresholdSummary data frame",
      "topics": [
        "plotF1Measure"
      ]
    },
    {
      "page": "plotGeneralizability",
      "title": "Plot the train/test generalizability diagnostic",
      "topics": [
        "plotGeneralizability"
      ]
    },
    {
      "page": "plotLearningCurve",
      "title": "plotLearningCurve",
      "topics": [
        "plotLearningCurve"
      ]
    },
    {
      "page": "plotNetBenefit",
      "title": "Plot the net benefit",
      "topics": [
        "plotNetBenefit"
      ]
    },
    {
      "page": "plotPlp",
      "title": "Plot all the PatientLevelPrediction plots",
      "topics": [
        "plotPlp"
      ]
    },
    {
      "page": "plotPrecisionRecall",
      "title": "Plot the precision-recall curve using the sparse thresholdSummary data frame",
      "topics": [
        "plotPrecisionRecall"
      ]
    },
    {
      "page": "plotPredictedPDF",
      "title": "Plot the Predicted probability density function, showing prediction overlap between true and false cases",
      "topics": [
        "plotPredictedPDF"
      ]
    },
    {
      "page": "plotPredictionDistribution",
      "title": "Plot the side-by-side boxplots of prediction distribution, by class",
      "topics": [
        "plotPredictionDistribution"
      ]
    },
    {
      "page": "plotPreferencePDF",
      "title": "Plot the preference score probability density function, showing prediction overlap between true and false cases #'",
      "topics": [
        "plotPreferencePDF"
      ]
    },
    {
      "page": "plotSmoothCalibration",
      "title": "Plot the smooth calibration as detailed in Calster et al. \"A calibration heirarchy for risk models was defined: from utopia to empirical data\" (2016)",
      "topics": [
        "plotSmoothCalibration"
      ]
    },
    {
      "page": "plotSparseCalibration",
      "title": "Plot the calibration",
      "topics": [
        "plotSparseCalibration"
      ]
    },
    {
      "page": "plotSparseCalibration2",
      "title": "Plot the conventional calibration",
      "topics": [
        "plotSparseCalibration2"
      ]
    },
    {
      "page": "plotSparseRoc",
      "title": "Plot the ROC curve using the sparse thresholdSummary data frame",
      "topics": [
        "plotSparseRoc"
      ]
    },
    {
      "page": "plotVariableScatterplot",
      "title": "Plot the variable importance scatterplot",
      "topics": [
        "plotVariableScatterplot"
      ]
    },
    {
      "page": "predictCyclops",
      "title": "Create predictive probabilities",
      "topics": [
        "predictCyclops"
      ]
    },
    {
      "page": "predictGlm",
      "title": "predict using a logistic regression model",
      "topics": [
        "predictGlm"
      ]
    },
    {
      "page": "predictPlp",
      "title": "predictPlp",
      "topics": [
        "predictPlp"
      ]
    },
    {
      "page": "preprocessData",
      "title": "A function that wraps around FeatureExtraction::tidyCovariateData to normalise the data and remove rare or redundant features",
      "topics": [
        "preprocessData"
      ]
    },
    {
      "page": "print.plpData",
      "title": "Print a plpData object",
      "topics": [
        "print.plpData"
      ]
    },
    {
      "page": "print.summary.plpData",
      "title": "Print a summary.plpData object",
      "topics": [
        "print.summary.plpData"
      ]
    },
    {
      "page": "recalibratePlp",
      "title": "recalibratePlp",
      "topics": [
        "recalibratePlp"
      ]
    },
    {
      "page": "recalibratePlpRefit",
      "title": "recalibratePlpRefit",
      "topics": [
        "recalibratePlpRefit"
      ]
    },
    {
      "page": "runMultiplePlp",
      "title": "Run a list of predictions analyses",
      "topics": [
        "runMultiplePlp"
      ]
    },
    {
      "page": "runPlp",
      "title": "runPlp - Develop and internally evaluate a model using specified settings",
      "topics": [
        "runPlp"
      ]
    },
    {
      "page": "savePlpAnalysesJson",
      "title": "Save the modelDesignList to a json file",
      "topics": [
        "savePlpAnalysesJson"
      ]
    },
    {
      "page": "savePlpData",
      "title": "Save the plpData to folder",
      "topics": [
        "savePlpData"
      ]
    },
    {
      "page": "savePlpModel",
      "title": "Saves the plp model",
      "topics": [
        "savePlpModel"
      ]
    },
    {
      "page": "savePlpResult",
      "title": "Saves the result from runPlp into the location directory",
      "topics": [
        "savePlpResult"
      ]
    },
    {
      "page": "savePlpShareable",
      "title": "Save the plp result as json files and csv files for transparent sharing",
      "topics": [
        "savePlpShareable"
      ]
    },
    {
      "page": "savePrediction",
      "title": "Saves the prediction dataframe to a json file",
      "topics": [
        "savePrediction"
      ]
    },
    {
      "page": "setAdaBoost",
      "title": "Create setting for AdaBoost with python DecisionTreeClassifier base estimator",
      "topics": [
        "setAdaBoost"
      ]
    },
    {
      "page": "setCoxModel",
      "title": "Create setting for lasso Cox model",
      "topics": [
        "setCoxModel"
      ]
    },
    {
      "page": "setDecisionTree",
      "title": "Create setting for the scikit-learn DecisionTree with python",
      "topics": [
        "setDecisionTree"
      ]
    },
    {
      "page": "setGradientBoostingMachine",
      "title": "Create setting for gradient boosting machine model using gbm_xgboost implementation",
      "topics": [
        "setGradientBoostingMachine"
      ]
    },
    {
      "page": "setIterativeHardThresholding",
      "title": "Create setting for Iterative Hard Thresholding model",
      "topics": [
        "setIterativeHardThresholding"
      ]
    },
    {
      "page": "setLassoLogisticRegression",
      "title": "Create modelSettings for lasso logistic regression",
      "topics": [
        "setLassoLogisticRegression"
      ]
    },
    {
      "page": "setLightGBM",
      "title": "Create setting for gradient boosting machine model using lightGBM (https://github.com/microsoft/LightGBM/tree/master/R-package).",
      "topics": [
        "setLightGBM"
      ]
    },
    {
      "page": "setMLP",
      "title": "Create setting for neural network model with python's scikit-learn. For bigger models, consider using 'DeepPatientLevelPrediction' package.",
      "topics": [
        "setMLP"
      ]
    },
    {
      "page": "setNaiveBayes",
      "title": "Create setting for naive bayes model with python",
      "topics": [
        "setNaiveBayes"
      ]
    },
    {
      "page": "setPythonEnvironment",
      "title": "Use the python environment created using configurePython()",
      "topics": [
        "setPythonEnvironment"
      ]
    },
    {
      "page": "setRandomForest",
      "title": "Create setting for random forest model using sklearn",
      "topics": [
        "setRandomForest"
      ]
    },
    {
      "page": "setRidgeRegression",
      "title": "Create modelSettings for ridge logistic regression",
      "topics": [
        "setRidgeRegression"
      ]
    },
    {
      "page": "setSVM",
      "title": "Create setting for the python sklearn SVM (SVC function)",
      "topics": [
        "setSVM"
      ]
    },
    {
      "page": "simulatePlpData",
      "title": "Generate simulated data",
      "topics": [
        "simulatePlpData"
      ]
    },
    {
      "page": "simulationProfile",
      "title": "A simulation profile for generating synthetic patient level prediction data",
      "topics": [
        "simulationProfile"
      ]
    },
    {
      "page": "sklearnFromJson",
      "title": "Loads sklearn python model from json",
      "topics": [
        "sklearnFromJson"
      ]
    },
    {
      "page": "sklearnToJson",
      "title": "Saves sklearn python model object to json in path",
      "topics": [
        "sklearnToJson"
      ]
    },
    {
      "page": "splitData",
      "title": "Split the plpData into test/train sets using a splitting settings of class 'splitSettings'",
      "topics": [
        "splitData"
      ]
    },
    {
      "page": "summary.plpData",
      "title": "Summarize a plpData object",
      "topics": [
        "summary.plpData"
      ]
    },
    {
      "page": "toSparseM",
      "title": "Convert the plpData in COO format into a sparse R matrix",
      "topics": [
        "toSparseM"
      ]
    },
    {
      "page": "validateExternal",
      "title": "validateExternal - Validate model performance on new data",
      "topics": [
        "validateExternal"
      ]
    },
    {
      "page": "validateMultiplePlp",
      "title": "externally validate the multiple plp models across new datasets",
      "topics": [
        "validateMultiplePlp"
      ]
    },
    {
      "page": "viewDatabaseResultPlp",
      "title": "open a local shiny app for viewing the result of a PLP analyses from a database",
      "topics": [
        "viewDatabaseResultPlp"
      ]
    },
    {
      "page": "viewMultiplePlp",
      "title": "open a local shiny app for viewing the result of a multiple PLP analyses",
      "topics": [
        "viewMultiplePlp"
      ]
    },
    {
      "page": "viewPlp",
      "title": "viewPlp - Interactively view the performance and model settings",
      "topics": [
        "viewPlp"
      ]
    }
  ],
  "_readme": "https://github.com/ohdsi/patientlevelprediction/raw/HEAD/README.md",
  "_rundeps": [
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  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.10+7-1~24.04",
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  ],
  "_vignettes": [
    {
      "source": "AddingCustomSplitting.Rmd",
      "filename": "AddingCustomSplitting.html",
      "title": "Adding Custom Data Splitting",
      "author": "Jenna Reps",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Data Splitting Function Code Structure",
        "Example",
        "Create function",
        "Implement function",
        "Acknowledgments"
      ],
      "created": "2022-03-11 14:13:13",
      "modified": "2025-02-06 10:15:34",
      "commits": 3
    },
    {
      "source": "AddingCustomFeatureEngineering.Rmd",
      "filename": "AddingCustomFeatureEngineering.html",
      "title": "Adding Custom Feature Engineering Functions",
      "author": "Jenna Reps, Egill Fridgeirsson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Feature Engineering Function Code Structure",
        "Example",
        "Create function",
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      "created": "2022-03-11 14:13:13",
      "modified": "2025-02-06 10:15:34",
      "commits": 5
    },
    {
      "source": "AddingCustomModels.Rmd",
      "filename": "AddingCustomModels.html",
      "title": "Adding Custom Patient-Level Prediction Algorithms",
      "author": "Jenna Reps, Martijn J. Schuemie, Patrick B. Ryan, Peter R. Rijnbeek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Algorithm Code Structure",
        "Set",
        "Fit",
        "Predict",
        "VarImp",
        "Algorithm Example",
        "Variable importance",
        "Acknowledgments"
      ],
      "created": "2022-03-11 14:13:13",
      "modified": "2026-03-09 13:25:16",
      "commits": 6
    },
    {
      "source": "AddingCustomSamples.Rmd",
      "filename": "AddingCustomSamples.html",
      "title": "Adding Custom Sampling Functions",
      "author": "Jenna Reps",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Sample Function Code Structure",
        "Example",
        "Create function",
        "Implement function",
        "Acknowledgments"
      ],
      "created": "2022-03-11 14:13:13",
      "modified": "2025-02-06 10:15:34",
      "commits": 3
    },
    {
      "source": "BuildingMultiplePredictiveModels.Rmd",
      "filename": "BuildingMultiplePredictiveModels.html",
      "title": "Automatically Build Multiple Patient-Level Predictive Models",
      "author": "Jenna Reps, Martijn J. Schuemie, Patrick B. Ryan, Peter R. Rijnbeek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Creating a model design",
        "Model design example 1",
        "Model design example 2",
        "Model design example 3",
        "Running multiple models",
        "Validating multiple models",
        "Viewing the results",
        "Acknowledgments"
      ],
      "created": "2018-10-05 14:57:54",
      "modified": "2025-02-11 12:13:08",
      "commits": 9
    },
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      "source": "BenchmarkTasks.Rmd",
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      "author": "Jenna Reps, Ross Williams, Peter R. Rijnbeek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Benchmark Tasks For Large-Scale Empirical Analyses"
      ],
      "created": "2023-10-12 13:04:56",
      "modified": "2025-02-06 10:15:34",
      "commits": 4
    },
    {
      "source": "BestPractices.Rmd",
      "filename": "BestPractices.html",
      "title": "Best Practice Research",
      "author": "Jenna Reps, Peter R. Rijnbeek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Best practice publications using the OHDSI PatientLevelPrediction framework"
      ],
      "created": "2025-02-06 10:15:34",
      "modified": "2025-02-11 12:13:08",
      "commits": 2
    },
    {
      "source": "BuildingPredictiveModels.Rmd",
      "filename": "BuildingPredictiveModels.html",
      "title": "Building patient-level predictive models",
      "author": "Jenna Reps, Martijn J. Schuemie, Patrick B. Ryan, Peter R. Rijnbeek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Study specification",
        "Problem definition 1: Stroke in atrial fibrilation patients",
        "Problem definition 2: Angioedema in ACE inhibitor users",
        "Study population definition",
        "Model development settings",
        "Example 1: Stroke in Atrial fibrillation patients",
        "Study Specification",
        "Study implementation",
        "Cohort instantiation",
        "ATLAS cohort builder",
        "Custom cohorts",
        "Study script creation",
        "Data extraction",
        "Additional inclusion criteria",
        "Splitting the data into training/validation/testing datasets",
        "Preprocessing the training data",
        "Model Development",
        "Example 2: Angioedema in ACE inhibitor users",
        "Spliting the data into training/validation/testing datasets",
        "Study package creation",
        "Internal validation",
        "Discrimination",
        "Smooth Calibration",
        "Other functionality",
        "Demos",
        "Acknowledgments",
        "Appendix 1: Study population settings details"
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