Man pages for hxia/plp-git-demo
Package for patient level prediction using data in the OMOP Common Data Model
| accuracy | Calculate the accuracy |
| applyEnsembleModel | Apply trained ensemble model on new data Apply a Patient... |
| applyModel | Apply train model on new data Apply a Patient Level... |
| averagePrecision | Calculate the average precision |
| brierScore | brierScore |
| calibrationLine | calibrationLine |
| checkPlpInstallation | Check PatientLevelPrediction and its dependencies are... |
| combinePlpModelSettings | combine two objects specifying multiple Plp model settings |
| computeAuc | Compute the area under the ROC curve |
| computeAucFromDataFrames | Compute the area under the ROC curve |
| configurePython | Sets up a virtual environment to use for PLP (can be conda or... |
| createLearningCurve | createLearningCurve |
| createLearningCurvePar | createLearningCurvePar |
| createLrSql | Convert logistic regression model to sql code... |
| createPlpJournalDocument | createPlpJournalDocument |
| createPlpModelSettings | create a an object specifying the multiple Plp model settings |
| createPlpReport | createPlpReport |
| createStudyPopulation | Create a study population |
| createStudyPopulationSettings | create the study population settings |
| diagnostic | diagnostic - Investigates the prediction problem settings -... |
| diagnosticOddsRatio | Calculate the diagnostic odds ratio |
| drawAttritionDiagramPlp | Draw the attrition diagram |
| evaluateMultiplePlp | externally validate the multiple plp models across new... |
| evaluatePlp | evaluatePlp |
| externalValidatePlp | externalValidatePlp - Validate a model on new databases |
| f1Score | Calculate the f1Score |
| falseDiscoveryRate | Calculate the falseDiscoveryRate |
| falseNegativeRate | Calculate the falseNegativeRate |
| falseOmissionRate | Calculate the falseOmissionRate |
| falsePositiveRate | Calculate the falsePositiveRate |
| fitGLMModel | Fit a predictive model |
| fitPlp | fitPlp |
| getAttritionTable | Get the attrition table for a population |
| getCalibration | Get a sparse summary of the calibration |
| getPlpData | Get the patient level prediction data from the server |
| getPlpTable | Create a dataframe with the summary details of the population... |
| getPredictionDistribution | Calculates the prediction distribution |
| getThresholdSummary | Calculate all measures for sparse ROC |
| interpretInstallCode | Tells you the package issue |
| launchDiagnosticsExplorer | Launch the Diagnostics Explorer Shiny app |
| listAppend | join two lists |
| loadEnsemblePlpModel | loads the Ensmeble plp model and return a model list |
| loadEnsemblePlpResult | loads the Ensemble plp results |
| loadPlpData | Load the cohort data from a folder |
| loadPlpFromCsv | Loads parts of the plp result saved as csv files for... |
| loadPlpModel | loads the plp model |
| loadPlpResult | Loads the evalaution dataframe |
| loadPrediction | Loads the prediciton dataframe to csv |
| loadPredictionAnalysisList | Load the multiple prediction json settings from a file |
| negativeLikelihoodRatio | Calculate the negativeLikelihoodRatio |
| negativePredictiveValue | Calculate the negativePredictiveValue |
| outcomeSurvivalPlot | Plot the outcome incidence over time |
| PatientLevelPrediction | PatientLevelPrediction |
| personSplitter | Split data into random subsets stratified by class |
| 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,... |
| plotRoc | Plot the ROC curve |
| 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 |
| predictAndromeda | Generated predictions from a regression model |
| predictPlp | predictPlp |
| predictProbabilities | Create predictive probabilities |
| randomSplitter | Split data into random subsets stratified by class |
| registerParallelBackend | registerParallelBackend |
| registerSequentialBackend | registerSequentialBackend |
| runEnsembleModel | ensemble - Create an ensembling model using different models |
| runPlp | runPlp - Train and evaluate the model |
| runPlpAnalyses | Run a list of predictions |
| saveEnsemblePlpModel | saves the Ensmeble plp model |
| saveEnsemblePlpResult | saves the Ensemble plp results |
| savePlpData | Save the cohort data to folder |
| savePlpModel | Saves the plp model |
| savePlpResult | Saves the result from runPlp into the location directory |
| savePlpToCsv | Save parts of the plp result as a csv for transparent sharing |
| savePrediction | Saves the prediction dataframe to RDS |
| savePredictionAnalysisList | Saves a json prediction settings given R settings |
| sensitivity | Calculate the sensitivity |
| setAdaBoost | Create setting for AdaBoost with python |
| setCIReNN | Create setting for CIReNN model |
| setCNNTorch | Create setting for CNN model with python |
| setCovNN | Create setting for multi-resolution CovNN model (stucture... |
| setCovNN2 | Create setting for CovNN2 model - convolution across input... |
| setCoxModel | Create setting for lasso Cox model |
| setDecisionTree | Create setting for DecisionTree with python |
| setDeepNN | Create setting for DeepNN model |
| setGBMSurvival | Create setting for GBM Survival with python #' @description... |
| setGradientBoostingMachine | Create setting for gradient boosting machine model using... |
| setKNN | Create setting for knn model |
| setLassoLogisticRegression | Create setting for lasso logistic regression |
| setLRTorch | Create setting for logistics regression model with python |
| setMLP | Create setting for neural network model with python |
| setMLPTorch | 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... |
| setRandomForestQuantileRegressor | Create setting for RandomForestQuantileRegressor with python... |
| setRNNTorch | Create setting for RNN model with python |
| setSagemakerBinary | Create setting for sagemaker model |
| setSVM | Create setting for SVM with python |
| similarPlpData | Extract new plpData using plpModel settings use metadata in... |
| simulatePlpData | Generate simulated data |
| specificity | Calculate the specificity |
| subjectSplitter | Split data when patients are in the data multiple times such... |
| timeSplitter | Split test/train data by time and then partitions training... |
| toSparseM | Convert the plpData in COO format into a sparse R matrix |
| toSparseTorchPython | Convert the plpData in COO format into a sparse python matrix... |
| transferLearning | [Under development] Transfer learning |
| transportModel | Transports a plpModel to a new location and removes sensitive... |
| transportPlp | Transports a plpResult to a new location and removed... |
| viewMultiplePlp | open a local shiny app for viewing the result of a multiple... |
| viewPlp | viewPlp - Interactively view the performance and model... |
