Package: pec 2023.04.12
pec: Prediction Error Curves for Risk Prediction Models in Survival Analysis
Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation. Most of the 'pec' functionality has been moved to 'riskRegression'.
Authors:
pec_2023.04.12.tar.gz
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pec.pdf |pec.html✨
pec/json (API)
| # Install 'pec' in R: |
| install.packages('pec', repos = c('https://tagteam.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tagteam/pec/issues
Last updated 2 years agofrom:0648d7ce1f. Checks:OK: 1 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 04 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 04 2024 |
Exports:calPlotcindexcoxboostcrpsibsipcwpecpecCforestpecCtreepecRpartplotPredictEventProbplotPredictSurvProbpredictEventProbpredictLifeYearsLostpredictRestrictedMeanTimepredictSurvProbR2resolvesplitMethodselectCoxsimCost
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercmprskcodetoolscolorspacedata.tablediagramdigestdoParallelevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsfuturefuture.applyggplot2globalsgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixMatrixModelsmemoisemetsmgcvmimemultcompmunsellmvtnormnlmennetnumDerivparallellypillarpkgconfigplotrixpolsplineprodlimprogressrPublishquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenriskRegressionrlangrmarkdownrmsrpartrstudioapisandwichsassscalesshapeSparseMSQUAREMstringistringrsurvivalTH.datatibbletimeregtinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calibration plots for right censored data | calPlot |
| Concordance index for right censored survival time data | cindex |
| Copenhagen Stroke Study | cost |
| Formula interface for function 'CoxBoost' of package 'CoxBoost'. | coxboost |
| Summarizing prediction error curves | crps ibs |
| German Breast Cancer Study Group 2 | GBSG2 |
| Estimation of censoring probabilities | ipcw ipcw.aalen ipcw.cox ipcw.marginal ipcw.none ipcw.nonpar |
| Pbc3 data | Pbc3 |
| Prediction error curves | pec |
| S3-wrapper function for cforest from the party package | pecCforest |
| S3-Wrapper for ctree. | pecCtree |
| Predict survival based on rpart tree object | pecRpart |
| Plot objects obtained with 'calPlot' | plot.calibrationPlot |
| Plotting prediction error curves | plot.pec |
| Plotting predicted survival curves. | plotPredictEventProb |
| Plotting predicted survival curves. | plotPredictSurvProb |
| Predicting event probabilities (cumulative incidences) in competing risk models. | predictEventProb predictEventProb.CauseSpecificCox predictEventProb.FGR predictEventProb.prodlim predictEventProb.rfsrc predictEventProb.riskRegression |
| Predicting life years lost (cumulative cumulative incidences) in competing risk models. | predictLifeYearsLost predictLifeYearsLost.CauseSpecificCox predictLifeYearsLost.FGR predictLifeYearsLost.prodlim predictLifeYearsLost.rfsrc predictLifeYearsLost.riskRegression |
| Predicting restricted mean time | predictRestrictedMeanTime predictRestrictedMeanTime.aalen predictRestrictedMeanTime.cox.aalen predictRestrictedMeanTime.coxph predictRestrictedMeanTime.cph predictRestrictedMeanTime.default predictRestrictedMeanTime.matrix predictRestrictedMeanTime.pecCtree predictRestrictedMeanTime.pecRpart predictRestrictedMeanTime.prodlim predictRestrictedMeanTime.psm predictRestrictedMeanTime.rfsrc predictRestrictedMeanTime.riskRegression predictRestrictedMeanTime.selectCox predictRestrictedMeanTime.survfit |
| Predicting survival probabilities | predictSurvProb predictSurvProb.aalen predictSurvProb.cox.aalen predictSurvProb.coxph predictSurvProb.cph predictSurvProb.default predictSurvProb.matrix predictSurvProb.pecCforest predictSurvProb.pecCtree predictSurvProb.pecRpart predictSurvProb.prodlim predictSurvProb.psm predictSurvProb.rfsrc predictSurvProb.riskRegression predictSurvProb.selectCox predictSurvProb.survfit |
| Printing a `pec' (prediction error curve) object. | print.pec summary.pec |
| Explained variation for survival models | R2 |
| Retrospective risk reclassification table | reclass |
| Resolve the splitMethod for estimation of prediction performance | resolvesplitMethod |
| Backward variable selection in the Cox regression model | selectCox |
| Stepwise variable selection in the Fine & Gray regression competing risk model | selectFGR |
| Simulate COST alike data | simCost |
| Drawing bootstrapped cross-validation curves and the .632 or .632plus error of models. The prediction error for an optional benchmark model can be added together with bootstrapped cross-validation error and apparent errors. | Special |
| threecity data | threecity |
