calPlotcindexcostcoxboostcrpsGBSG2ipcwPbc3pecpecCforestplot.pecplotPredictEventProbplotPredictSurvProbpredictEventProbpredictLifeYearsLostpredictSurvProbprint.pecR2resolvesplitMethodselectCoxselectFGRsimCostSpecialIndexPackage ‘pec’September 5, 2014Title Prediction Error Curves for Survival ModelsVersion 2.3.7Author Thomas A. GerdsDescription Validation of predicted survival probabilities using inverse weighting and resampling.Depends R (>= 1.9.1)Imports prodlim, foreach, rms, survivalSuggests timereg, randomForestSRC, party, cmprsk, rpart, doMC,CoxBoost, crrstep, riskRegres-sion, lava, HmiscMaintainer Thomas A. Gerds <[email protected]>License GPL (>= 2)NeedsCompilation yesRepository CRANDate/Publication 2014-09-05 17:51:01R topics documented:calPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cindex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5cost . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9coxboost . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10crps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11GBSG2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12ipcw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Pbc3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15pec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17pecCforest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24plot.pec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25plotPredictEventProb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2712 calPlotplotPredictSurvProb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29predictEventProb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30predictLifeYearsLost . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32predictSurvProb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33print.pec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35R2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36resolvesplitMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38selectCox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39selectFGR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40simCost . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Special . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Index 44calPlot Calibration plots for right censored dataDescriptionCalibration plots for risk prediction models in right censored survival and competing risks dataUsagecalPlot(object, time, formula, data, splitMethod = "none", B = 1, M,outcome = c("pseudo", "prodlim"), showPseudo, pseudo.col = NULL,pseudo.pch = NULL, method = "nne", round = TRUE, bandwidth = NULL,q = 10, jack.density = 55, add = FALSE, diag = !add, legend = !add,axes = !add, xlim, ylim, xlab = "Predicted event probability",ylab = "Pseudo-observed event status", col, lwd, lty, pch, cause = 1,percent = TRUE, giveToModel = NULL, na.action = na.fail, cores = 1,verbose = FALSE, ...)Argumentsobject A named list of prediction models, where allowed entries are (1) R-objects forwhich a predictSurvProb method exists (see details), (2) a call that evaluates tosuch an R-object (see examples), (3) a matrix with predicted probabilities havingas many rows as data and as many columns as times. For cross-validation allobjects in this list must include their call.time The evaluation …