accuracy | Calculate the accuracy |
addDiagnosePlpToDatabase | Insert a diagnostic result into a PLP result schema database |
addMultipleDiagnosePlpToDatabase | Insert mutliple diagnosePlp results saved to a directory into... |
addMultipleRunPlpToDatabase | Populate the PatientLevelPrediction results tables |
addRunPlpToDatabase | Function to add the run plp (development or validation) to... |
averagePrecision | Calculate the average precision |
brierScore | brierScore |
calibrationLine | calibrationLine |
computeAuc | Compute the area under the ROC curve |
computeGridPerformance | Computes grid performance with a specified performance... |
configurePython | Sets up a virtual environment to use for PLP (can be conda or... |
covariateSummary | covariateSummary |
createCohortCovariateSettings | Extracts covariates based on cohorts |
createDatabaseDetails | Create a setting that holds the details about the cdmDatabase... |
createDatabaseList | Create a list with the database details and database meta... |
createDatabaseSchemaSettings | Create the PatientLevelPrediction database result schema... |
createDefaultExecuteSettings | Creates default list of settings specifying what parts of... |
createDefaultSplitSetting | Create the settings for defining how the plpData are split... |
createExecuteSettings | Creates list of settings specifying what parts of runPlp to... |
createFeatureEngineeringSettings | Create the settings for defining any feature engineering that... |
createLearningCurve | createLearningCurve |
createLogSettings | Create the settings for logging the progression of the... |
createModelDesign | Specify settings for deceloping a single model |
createPlpResultTables | Create the results tables to store PatientLevelPrediction... |
createPreprocessSettings | Create the settings for preprocessing the trainData. |
createRandomForestFeatureSelection | Create the settings for random foreat based feature selection |
createRestrictPlpDataSettings | createRestrictPlpDataSettings define extra restriction... |
createSampleSettings | Create the settings for defining how the trainData from... |
createSplineSettings | Create the settings for adding a spline for continuous... |
createStratifiedImputationSettings | Create the settings for adding a spline for continuous... |
createStudyPopulation | Create a study population |
createStudyPopulationSettings | create the study population settings |
createTempModelLoc | Create a temporary model location |
createUnivariateFeatureSelection | Create the settings for defining any feature selection that... |
createValidationSettings | createValidationSettings define optional settings for... |
diagnoseMultiplePlp | Run a list of predictions diagnoses |
diagnosePlp | diagnostic - Investigates the prediction problem settings -... |
diagnosticOddsRatio | Calculate the diagnostic odds ratio |
evaluatePlp | evaluatePlp |
externalValidateDbPlp | externalValidateDbPlp - Validate a model on new databases |
extractDatabaseToCsv | Exports all the results from a database into csv files |
f1Score | Calculate the f1Score |
falseDiscoveryRate | Calculate the falseDiscoveryRate |
falseNegativeRate | Calculate the falseNegativeRate |
falseOmissionRate | Calculate the falseOmissionRate |
falsePositiveRate | Calculate the falsePositiveRate |
fitPlp | fitPlp |
getCalibrationSummary | Get a sparse summary of the calibration |
getCohortCovariateData | Extracts covariates based on cohorts |
getDemographicSummary | Get a calibration per age/gender groups |
getPlpData | Get the patient level prediction data from the server |
getPredictionDistribution | Calculates the prediction distribution |
getPredictionDistribution_binary | Calculates the prediction distribution |
getThresholdSummary | Calculate all measures for sparse ROC |
getThresholdSummary_binary | Calculate all measures for sparse ROC when prediction is... |
ici | Calculate the Integrated Calibration Information from Austin... |
insertCsvToDatabase | Function to insert results into a database from csvs |
insertModelDesignInDatabase | Insert a model design into a PLP result schema database |
insertResultsToSqlite | Create sqlite database with the results |
listAppend | join two lists |
listCartesian | Cartesian product |
loadPlpAnalysesJson | Load the multiple prediction json settings from a file |
loadPlpData | Load the cohort data 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... |
loadPrediction | Loads the prediciton dataframe to csv |
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... |
negativeLikelihoodRatio | Calculate the negativeLikelihoodRatio |
negativePredictiveValue | Calculate the negativePredictiveValue |
outcomeSurvivalPlot | Plot the outcome incidence over time |
PatientLevelPrediction | PatientLevelPrediction |
pfi | pfi |
plotDemographicSummary | Plot the Observed vs. expected incidence, by age and gender |
plotF1Measure | Plot the F1 measure efficiency frontier using the sparse... |
plotGeneralizability | Plot the train/test generalizability diagnostic |
plotLearningCurve | plotLearningCurve |
plotPlp | Plot all the PatientLevelPrediction plots |
plotPrecisionRecall | Plot the precision-recall curve using the sparse... |
plotPredictedPDF | Plot the Predicted probability density function, showing... |
plotPredictionDistribution | Plot the side-by-side boxplots of prediction distribution, by... |
plotPreferencePDF | Plot the preference score probability density function,... |
plotSmoothCalibration | Plot the smooth calibration as detailed in Calster et al. "A... |
plotSparseCalibration | Plot the calibration |
plotSparseCalibration2 | Plot the conventional calibration |
plotSparseRoc | Plot the ROC curve using the sparse thresholdSummary data... |
plotVariableScatterplot | Plot the variable importance scatterplot |
plpDataSimulationProfile | A simulation profile |
positiveLikelihoodRatio | Calculate the positiveLikelihoodRatio |
positivePredictiveValue | Calculate the positivePredictiveValue |
predictCyclops | Create predictive probabilities |
predictPlp | predictPlp |
preprocessData | A function that wraps around... |
recalibratePlp | recalibratePlp |
recalibratePlpRefit | recalibratePlpRefit |
runMultiplePlp | Run a list of predictions analyses |
runPlp | runPlp - Develop and internally evaluate a model using... |
savePlpAnalysesJson | Save the modelDesignList to a json file |
savePlpData | Save the cohort data 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... |
savePrediction | Saves the prediction dataframe to RDS |
sensitivity | Calculate the sensitivity |
setAdaBoost | Create setting for AdaBoost with python... |
setCoxModel | Create setting for lasso Cox model |
setDecisionTree | Create setting for the scikit-learn 1.0.1 DecisionTree with... |
setGradientBoostingMachine | Create setting for gradient boosting machine model using... |
setIterativeHardThresholding | Create setting for lasso logistic regression |
setKNN | Create setting for knn model |
setLassoLogisticRegression | Create setting for lasso logistic regression |
setLightGBM | Create setting for gradient boosting machine model using... |
setMLP | Create setting for neural network model with python |
setNaiveBayes | Create setting for naive bayes model with python |
setPythonEnvironment | Use the virtual environment created using configurePython() |
setRandomForest | Create setting for random forest model with python (very... |
setSVM | Create setting for the python sklearn SVM (SVC function) |
simulatePlpData | Generate simulated data |
sklearnFromJson | Loads sklearn python model from json |
sklearnToJson | Saves sklearn python model object to json in path |
specificity | Calculate the specificity |
splitData | Split the plpData into test/train sets using a splitting... |
toSparseM | Convert the plpData in COO format into a sparse R matrix |
validateMultiplePlp | externally validate the multiple plp models across new... |
viewDatabaseResultPlp | open a local shiny app for viewing the result of a PLP... |
viewMultiplePlp | open a local shiny app for viewing the result of a multiple... |
viewPlp | viewPlp - Interactively view the performance and model... |
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