R: Develop Clinical Prediction Models Using the Common Data Model

# Develop Clinical Prediction Models Using the Common Data Model

## Documentation for package ‘PatientLevelPrediction’ version 6.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M O P R S T V

## -- A --

averagePrecision | Calculate the average precision

## -- B --

brierScore | brierScore

## -- C --

calibrationLine | calibrationLine
computeAuc | Compute the area under the ROC curve
computeAuprc | Compute the area under the Precision-Recall curve
computeGridPerformance | Computes grid performance for a hyperparameter combination (backwards compatible)
configurePython | Sets up a python environment to use for PLP (can be conda or venv)
covariateSummary | covariateSummary
createCohortCovariateSettings | Extracts covariates based on cohorts
createDatabaseDetails | Create a setting that holds the details about the cdmDatabase connection for data extraction
createDatabaseSchemaSettings | Create the PatientLevelPrediction database result schema settings
createDefaultExecuteSettings | Creates default list of settings specifying what parts of runPlp to execute
createDefaultSplitSetting | 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)
createExecuteSettings | Creates list of settings specifying what parts of runPlp to execute
createExistingSplitSettings | 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
createFeatureEngineeringSettings | Create the settings for defining any feature engineering that will be done
createGlmModel | createGlmModel
createHyperparameterSettings | Create Hyperparameter Settings
createIterativeImputer | Create Iterative Imputer settings
createLearningCurve | createLearningCurve
createLogSettings | Create the settings for logging the progression of the analysis
createModelDesign | Specify settings for developing a single model
createNormalizer | Create the settings for normalizing the data @param type The type of normalization to use, either "minmax" or "robust"
createPlpResultTables | Create the results tables to store PatientLevelPrediction models and results into a database
createPreprocessSettings | Create the settings for preprocessing the trainData.
createRandomForestFeatureSelection | Create the settings for random foreat based feature selection
createRareFeatureRemover | Create the settings for removing rare features
createRestrictPlpDataSettings | createRestrictPlpDataSettings define extra restriction settings when calling getPlpData
createSampleSettings | Create the settings for defining how the trainData from 'splitData' are sampled using default sample functions.
createSimpleImputer | Create Simple Imputer settings
createSklearnIterativeImputer | Create scikit-learn Iterative Imputer settings
createSklearnModel | Plug an existing scikit learn python model into the PLP framework
createSplineSettings | Create the settings for adding a spline for continuous variables
createStratifiedImputationSettings | Create the settings for using stratified imputation.
createStudyPopulation | Create a study population
createStudyPopulationSettings | create the study population settings
createTempModelLoc | Create a temporary model location
createTuningMetric | Create a tuning metric descriptor
createUnivariateFeatureSelection | Create the settings for defining any feature selection that will be done
createValidationDesign | createValidationDesign - Define the validation design for external validation
createValidationSettings | createValidationSettings define optional settings for performing external validation

## -- D --

diagnoseMultiplePlp | Run a list of predictions diagnoses
diagnosePlp | diagnostic - Investigates the prediction problem settings - use before training a model

## -- E --

evaluatePlp | evaluatePlp
externalValidateDbPlp | externalValidateDbPlp - Validate a model on new databases
extractDatabaseToCsv | Exports all the results from a database into csv files

## -- F --

fitPlp | fitPlp

## -- G --

getCalibrationSummary | Get a sparse summary of the calibration
getCohortCovariateData | Extracts covariates based on cohorts
getDemographicSummary | Get a demographic summary
getEunomiaPlpData | Create a plpData object from the Eunomia database'
getPlpData | Extract the patient level prediction data from the server
getPredictionDistribution | Calculates the prediction distribution
getThresholdSummary | Calculate all measures for sparse ROC

## -- I --

ici | Calculate the Integrated Calibration Index from Austin and Steyerberg https://onlinelibrary.wiley.com/doi/full/10.1002/sim.8281
insertCsvToDatabase | Function to insert results into a database from csvs
insertResultsToSqlite | Create sqlite database with the results

## -- L --

listAppend | join two lists
listCartesian | Cartesian product
loadPlpAnalysesJson | Load the multiple prediction json settings from a file
loadPlpData | Load the plpData from a folder
loadPlpModel | loads the plp model
loadPlpResult | Loads the evalaution dataframe
loadPlpShareable | Loads the plp result saved as json/csv files for transparent sharing
loadPrediction | Loads the prediction dataframe to json

## -- M --

MapIds | Map covariate and row Ids so they start from 1
migrateDataModel | Migrate Data model
modelBasedConcordance | 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/

## -- O --

outcomeSurvivalPlot | Plot the outcome incidence over time

## -- P --

pfi | Permutation Feature Importance
plotDemographicSummary | Plot the Observed vs. expected incidence, by age and gender
plotF1Measure | Plot the F1 measure efficiency frontier using the sparse thresholdSummary data frame
plotGeneralizability | Plot the train/test generalizability diagnostic
plotLearningCurve | plotLearningCurve
plotNetBenefit | Plot the net benefit
plotPlp | Plot all the PatientLevelPrediction plots
plotPrecisionRecall | Plot the precision-recall curve using the sparse thresholdSummary data frame
plotPredictedPDF | Plot the Predicted probability density function, showing prediction overlap between true and false cases
plotPredictionDistribution | Plot the side-by-side boxplots of prediction distribution, by class
plotPreferencePDF | Plot the preference score probability density function, showing prediction overlap between true and false cases #'
plotSmoothCalibration | Plot the smooth calibration as detailed in Calster et al. "A calibration heirarchy for risk models was defined: from utopia to empirical data" (2016)
plotSparseCalibration | Plot the calibration
plotSparseCalibration2 | Plot the conventional calibration
plotSparseRoc | Plot the ROC curve using the sparse thresholdSummary data frame
plotVariableScatterplot | Plot the variable importance scatterplot
predictCyclops | Create predictive probabilities
predictGlm | predict using a logistic regression model
predictPlp | predictPlp
preprocessData | A function that wraps around FeatureExtraction::tidyCovariateData to normalise the data and remove rare or redundant features
print.plpData | Print a plpData object
print.summary.plpData | Print a summary.plpData object

## -- R --

recalibratePlp | recalibratePlp
recalibratePlpRefit | recalibratePlpRefit
runMultiplePlp | Run a list of predictions analyses
runPlp | runPlp - Develop and internally evaluate a model using specified settings

## -- S --

savePlpAnalysesJson | Save the modelDesignList to a json file
savePlpData | Save the plpData to folder
savePlpModel | Saves the plp model
savePlpResult | Saves the result from runPlp into the location directory
savePlpShareable | Save the plp result as json files and csv files for transparent sharing
savePrediction | Saves the prediction dataframe to a json file
setAdaBoost | Create setting for AdaBoost with python DecisionTreeClassifier base estimator
setCoxModel | Create setting for lasso Cox model
setDecisionTree | Create setting for the scikit-learn DecisionTree with python
setGradientBoostingMachine | Create setting for gradient boosting machine model using gbm_xgboost implementation
setIterativeHardThresholding | Create setting for Iterative Hard Thresholding model
setLassoLogisticRegression | Create modelSettings for lasso logistic regression
setLightGBM | Create setting for gradient boosting machine model using lightGBM (https://github.com/microsoft/LightGBM/tree/master/R-package).
setMLP | Create setting for neural network model with python's scikit-learn. For bigger models, consider using 'DeepPatientLevelPrediction' package.
setNaiveBayes | Create setting for naive bayes model with python
setPythonEnvironment | Use the python environment created using configurePython()
setRandomForest | Create setting for random forest model using sklearn
setRidgeRegression | Create modelSettings for ridge logistic regression
setSVM | Create setting for the python sklearn SVM (SVC function)
simulatePlpData | Generate simulated data
simulationProfile | A simulation profile for generating synthetic patient level prediction data
sklearnFromJson | Loads sklearn python model from json
sklearnToJson | Saves sklearn python model object to json in path
splitData | Split the plpData into test/train sets using a splitting settings of class 'splitSettings'
summary.plpData | Summarize a plpData object

## -- T --

toSparseM | Convert the plpData in COO format into a sparse R matrix

## -- V --

validateExternal | validateExternal - Validate model performance on new data
validateMultiplePlp | externally validate the multiple plp models across new datasets
viewDatabaseResultPlp | open a local shiny app for viewing the result of a PLP analyses from a database
viewMultiplePlp | open a local shiny app for viewing the result of a multiple PLP analyses
viewPlp | viewPlp - Interactively view the performance and model settings