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:Thomas A. Gerds

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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

Datasets:

GBSG2 - German Breast Cancer Study Group 2
Pbc3 - Pbc3 data
cost - Copenhagen Stroke Study
threecity - Threecity data

On CRAN:

20 exports 5.72 score 103 dependencies 22 dependents 56 mentions 432 scripts 5.8k downloads

Last updated 1 years agofrom:0648d7ce1f. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win-x86_64	WARNING	Sep 05 2024
R-4.5-linux-x86_64	WARNING	Sep 05 2024
R-4.4-win-x86_64	WARNING	Sep 05 2024
R-4.4-mac-x86_64	WARNING	Sep 05 2024
R-4.4-mac-aarch64	WARNING	Sep 05 2024
R-4.3-win-x86_64	WARNING	Aug 06 2024
R-4.3-mac-x86_64	WARNING	Aug 06 2024
R-4.3-mac-aarch64	WARNING	Aug 06 2024

Exports:calPlot cindex coxboost crps ibs ipcw pec pecCforest pecCtree pecRpart plotPredictEventProb plotPredictSurvProb predictEventProb predictLifeYearsLost predictRestrictedMeanTime predictSurvProb R2 resolvesplitMethod selectCox simCost

Dependencies:backports base64enc bslib cachem checkmate cli cluster cmprsk codetools colorspace data.table diagram digest doParallel evaluate fansi farver fastmap fontawesome foreach foreign Formula fs future future.apply ggplot2 globals glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv magrittr MASS Matrix MatrixModels memoise mets mgcv mime multcomp munsell mvtnorm nlme nnet numDeriv parallelly pillar pkgconfig plotrix polspline prodlim progressr Publish quantreg R6 ranger rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen riskRegression rlang rmarkdown rms rpart rstudioapi sandwich sass scales shape SparseM SQUAREM stringi stringr survival TH.data tibble timereg tinytex utf8 vctrs viridis viridisLite withr xfun yaml zoo

Citation

Development and contributors

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