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.

AuthorThomas A. Gerds
Date of publication2016-05-14 23:19:27
MaintainerThomas A. Gerds <tag@biostat.ku.dk>
LicenseGPL (>= 2)
Version2.4.9

View on CRAN

Man pages

calPlot: Calibration plots for right censored data

cindex: Concordance index for right censored survival time data

cost: Copenhagen Stroke Study

coxboost: Formula interface for function 'CoxBoost' of package...

crps: Summarizing prediction error curves

GBSG2: German Breast Cancer Study Group 2

ipcw: Estimation of censoring probabilities

Pbc3: Pbc3 data

pec: Prediction error curves

pecCforest: S3-wrapper function for cforest from the party package

pecCtree: S3-Wrapper for ctree.

pecRpart: Predict survival based on rpart tree object

plot.calibrationPlot: Plot objects obtained with 'calPlot'

plot.pec: Plotting prediction error curves

plotPredictEventProb: Plotting predicted survival curves.

plotPredictSurvProb: Plotting predicted survival curves.

predictEventProb: Predicting event probabilities (cumulative incidences) in...

predictLifeYearsLost: Predicting life years lost (cumulative cumulative incidences)...

predictRestrictedMeanTime: Predicting restricted mean time

predictSurvProb: Predicting survival probabilities

print.pec: Printing a 'pec' (prediction error curve) object.

R2: Explained variation for survival models

reclass: Retrospective risk reclassification table

resolvesplitMethod: Resolve the splitMethod for estimation of prediction...

selectCox: Backward variable selection in the Cox regression model

selectFGR: Stepwise variable selection in the Fine & Gray regression...

simCost: Simulate COST alike data

Special: Drawing bootstrapped cross-validation curves and the .632 or...

threecity: threecity data

wallyPlot: Wally plots to assess calibration of a risk or survival...

Functions

calPlot Man page
cindex Man page
cost Man page
coxboost Man page
crps Man page
GBSG2 Man page
ibs Man page
ipcw Man page
ipcw.aalen Man page
ipcw.cox Man page
ipcw.marginal Man page
ipcw.none Man page
ipcw.nonpar Man page
Pbc3 Man page
pec Man page
pecCforest Man page
pecCtree Man page
pecRpart Man page
plot.calibrationPlot Man page
plot.pec Man page
plotPredictEventProb Man page
plotPredictSurvProb Man page
predictEventProb Man page
predictEventProb.CauseSpecificCox Man page
predictEventProb.FGR Man page
predictEventProb.prodlim Man page
predictEventProb.rfsrc Man page
predictEventProb.riskRegression Man page
predictLifeYearsLost Man page
predictLifeYearsLost.CauseSpecificCox Man page
predictLifeYearsLost.FGR Man page
predictLifeYearsLost.prodlim Man page
predictLifeYearsLost.rfsrc Man page
predictLifeYearsLost.riskRegression Man page
predictRestrictedMeanTime Man page
predictRestrictedMeanTime.aalen Man page
predictRestrictedMeanTime.cox.aalen Man page
predictRestrictedMeanTime.coxph Man page
predictRestrictedMeanTime.cph Man page
predictRestrictedMeanTime.default Man page
predictRestrictedMeanTime.matrix Man page
predictRestrictedMeanTime.pecCtree Man page
predictRestrictedMeanTime.pecRpart Man page
predictRestrictedMeanTime.prodlim Man page
predictRestrictedMeanTime.psm Man page
predictRestrictedMeanTime.rfsrc Man page
predictRestrictedMeanTime.riskRegression Man page
predictRestrictedMeanTime.selectCox Man page
predictRestrictedMeanTime.survfit Man page
predictSurvProb Man page
predictSurvProb.aalen Man page
predictSurvProb.cox.aalen Man page
predictSurvProb.coxph Man page
predictSurvProb.cph Man page
predictSurvProb.default Man page
predictSurvProb.matrix Man page
predictSurvProb.pecCforest Man page
predictSurvProb.pecCtree Man page
predictSurvProb.pecRpart Man page
predictSurvProb.prodlim Man page
predictSurvProb.psm Man page
predictSurvProb.rfsrc Man page
predictSurvProb.riskRegression Man page
predictSurvProb.selectCox Man page
predictSurvProb.survfit Man page
print.pec Man page
R2 Man page
reclass Man page
resolvesplitMethod Man page
selectCox Man page
selectFGR Man page
simCost Man page
Special Man page
summary.pec Man page
threecity Man page
wallyPlot Man page

Files

pec
pec/inst
pec/inst/CITATION
pec/tests
pec/tests/testthat
pec/tests/testthat/pec-loop.R
pec/src
pec/src/pec.c
pec/src/ccr.c
pec/src/cindex.c
pec/src/brier_score.c
pec/src/SNull.c
pec/src/auc.c
pec/src/pecResiduals.c
pec/src/survest_cox_aalen.c
pec/NAMESPACE
pec/data
pec/data/Pbc3.csv.gz
pec/data/cost.rda
pec/data/threecity.csv.gz
pec/data/GBSG2.csv.gz
pec/R
pec/R/testResiduals.R pec/R/print.vandeWielTest.R pec/R/predictSurvProb.R pec/R/plot.pec.R pec/R/predictEventProb.coxboost.R pec/R/print.R2.R pec/R/calPlot.R pec/R/summary.Cindex.R pec/R/pec-package.R pec/R/crps.R pec/R/kFoldCrossValidation.R pec/R/bootstrapCrossValidation.R pec/R/CindexBootstrapCrossValidation.R pec/R/allComparisons.R pec/R/pec.R pec/R/print.Cindex.R pec/R/summary.confScoreSurv.R pec/R/plot.CiCindex.R pec/R/predictRestrictedMeanTime.R pec/R/ipcw.R pec/R/R2.R pec/R/predictSurvProb.ctree.R pec/R/plot.calibrationPlot.R pec/R/predictEventProb.R pec/R/predictLandmark.R pec/R/CindexKFoldCrossValidation.R pec/R/predictSurvProb.pseudoForest.R pec/R/pseudo.kFoldCrossValidation.R pec/R/predictSurvProb.cforest.R pec/R/print.calibrationPlot.R pec/R/checkModels.R pec/R/summary.pec.R pec/R/survest.cox.aalen.R pec/R/print.ConfScoreSurv.R pec/R/resolveSplitMethod.R pec/R/selectCox.R pec/R/predictSurvProb.penfitS3.R pec/R/print.riskReclassification.R pec/R/print.method.R pec/R/ConfScoreSurv.R pec/R/plotPredictSurvProb.R pec/R/predictSurvProb.FastBw.R pec/R/ConfInt.Cindex.R pec/R/print.crps.R pec/R/baselineHazard.coxph.R pec/R/plot.Cindex.R pec/R/plot.riskReclassification.R pec/R/predictEventProb.pseudoForest.R pec/R/plotPredictEventProb.R pec/R/simCost.R pec/R/internalTalk.R pec/R/predictLifeYearsLost.R pec/R/print.splitMethod.R pec/R/predictEventProb.selectFGR.R pec/R/pseudoPecMethods.R pec/R/survest.aalen.R pec/R/reclass.R pec/R/cindex.R pec/R/plot.confScoreSurv.R pec/R/Dint.R pec/R/ibs.R pec/R/print.IPCW.R pec/R/pseudo.bootstrapCrossValidation.R pec/R/print.pec.R pec/R/print.multiSplitTest.R pec/R/marginal.prodlim.R pec/R/wallyPlot.R pec/R/Special.R pec/R/internalReevalFit.R
pec/MD5
pec/README
pec/DESCRIPTION
pec/man
pec/man/Special.Rd pec/man/crps.Rd pec/man/plot.pec.Rd pec/man/predictEventProb.Rd pec/man/GBSG2.Rd pec/man/threecity.Rd pec/man/cost.Rd pec/man/plotPredictSurvProb.Rd pec/man/pecCtree.Rd pec/man/calPlot.Rd pec/man/reclass.Rd pec/man/predictRestrictedMeanTime.Rd pec/man/wallyPlot.Rd pec/man/resolvesplitMethod.Rd pec/man/plotPredictEventProb.Rd pec/man/simCost.Rd pec/man/R2.Rd pec/man/selectFGR.Rd pec/man/selectCox.Rd pec/man/pec.Rd pec/man/predictSurvProb.Rd pec/man/print.pec.Rd pec/man/Pbc3.Rd pec/man/cindex.Rd pec/man/predictLifeYearsLost.Rd pec/man/pecCforest.Rd pec/man/pecRpart.Rd pec/man/ipcw.Rd pec/man/coxboost.Rd pec/man/plot.calibrationPlot.Rd

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