Package: timereg 2.0.6

timereg: Flexible Regression Models for Survival Data

Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, fast cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in the 'ahaz' package.

Authors:Thomas Scheike [aut, cre], Torben Martinussen [aut], Jeremy Silver [ctb], Klaus K. Holst [ctb]

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timereg/json (API)

# Install 'timereg' in R:
install.packages('timereg', repos = c('https://scheike.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/scheike/timereg/issues

Uses libs:
  • openblas– Optimized BLAS
Datasets:
  • TRACE - The TRACE study group of myocardial infarction
  • bmt - The Bone Marrow Transplant Data
  • cd4 - The multicenter AIDS cohort study
  • csl - CSL liver chirrosis data
  • diabetes - The Diabetic Retinopathy Data
  • mela.pop - Melanoma data and Danish population mortality by age and sex
  • melanoma - The Melanoma Survival Data
  • mypbc - My version of the PBC data of the survival package
  • sTRACE - The TRACE study group of myocardial infarction
  • tTRACE - The TRACE study group of myocardial infarction

On CRAN:

139 exports 29 stars 5.34 score 15 dependencies 40 dependents 10 mentions 250 scripts 7.9k downloads

Last updated 12 days agofrom:53fe9a56f0. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-win-x86_64OKSep 06 2024
R-4.5-linux-x86_64OKSep 06 2024
R-4.4-win-x86_64OKSep 06 2024
R-4.4-mac-x86_64OKSep 06 2024
R-4.4-mac-aarch64OKSep 06 2024
R-4.3-win-x86_64OKSep 06 2024
R-4.3-mac-x86_64OKSep 06 2024
R-4.3-mac-aarch64OKSep 06 2024

Exports:[.Eventaalenaalen.desaalen.des2aalenBaseaalenBaseCadditive.compSsas.character.Eventas.matrix.Eventcheck.missingcluster.index.timeregcoef.aalencoef.compriskcoef.comprisk.ipwcoef.cox.aalencoef.cox.ipwcoef.cox.margcoef.dynregcoef.resmeancoef.timecoxcoef.two.stagecoefBasecoefcoxcomp.riskcomprisk.ipwconstcoxcox.aalencox.aalenBasecox.ipwcox.margCpredCsmooth2BCsmoothBcum.residualsdynregdynregBaseEventevent.splitformat.EventGprop.oddsis.diagkmplotkrylow.plslocalTimeRegnameestimatenamematrixnames2formulapavapava.predpe.sasienipercenplot.aalenplot.compriskplot.cox.aalenplot.cum.residualsplot.cumsplot.dynregplot.predict.timeregplot.prop.excessplot.resmeanplot.restricted.residual.meanplot.timecoxplot.two.stageplotConfregionplotScorepred.cumpred.despred.stratKMpredict.aalenpredict.compriskpredict.cox.aalenpredict.timeregpredict.two.stagepredictpropoddsprep.comp.riskprep.glm.compriskprint.aalenprint.compriskprint.comprisk.ipwprint.cox.aalenprint.cox.ipwprint.cox.margprint.cum.residualsprint.dynregprint.Eventprint.pe.sasieniprint.predict.timeregprint.prop.excessprint.resmeanprint.timecoxprint.two.stagepropprop.excessprop.excessBaseprop.oddsprop.odds.subdistprop.odds.subdist.ipwpvalqcutrbind.Eventread.designread.survrecurrent.marginal.coxmeanrecurrent.marginal.meanres.meanresidualsTimeregrestricted.residual.meanrm.missingsemiaalensemicoxsemiregBasesindex.prodlimsummary.aalensummary.comprisksummary.comprisk.ipwsummary.cox.aalensummary.cox.ipwsummary.cox.margsummary.cum.residualssummary.dynregsummary.Eventsummary.pe.sasienisummary.predict.timeregsummary.prop.excesssummary.resmeansummary.restricted.residual.meansummary.timecoxsummary.two.stagetimecoxtimecoxBasetimereg.formulatimetesttwo.stagevcov.aalenvcov.comp.riskvcov.cox.aalenvcov.two.stagewald.test

Dependencies:clicodetoolsdigestfuturefuture.applyglobalslatticelavalistenvMatrixnumDerivparallellyprogressrSQUAREMsurvival

Readme and manuals

Help Manual

Help pageTopics
Fit additive hazards modelaalen
The Bone Marrow Transplant Databmt
The multicenter AIDS cohort studycd4
Competings Risks Regressioncomp.risk
Identifies parametric terms of modelconst
Identifies proportional excess terms of modelcox
Fit Cox-Aalen survival modelcox.aalen
Missing data IPW Coxcoef.cox.ipw cox.ipw print.cox.ipw summary.cox.ipw
CSL liver chirrosis datacsl
Model validation based on cumulative residualscum.residuals
The Diabetic Retinopathy Datadiabetes
Fit time-varying regression modeldynreg
Event history objectas.character.Event as.matrix.Event Event format.Event print.Event rbind.Event summary.Event [.Event
EventSplit (SurvSplit).event.split
Fit Generalized Semiparametric Proportional 0dds ModelGprop.odds
Fits Krylow based PLS for additive hazards modelkrylow.pls
Melanoma data and Danish population mortality by age and sexmela.pop
The Melanoma Survival Datamelanoma
my version of the PBC data of the survival packagemypbc
Make predictions of predict functions in rows mononotonepava.pred
Fits Proportional excess hazards model with fixed offsetspe.sasieni summary.pe-sasieni
Plots estimates and test-processesplot.aalen plot.cox.aalen plot.prop.excess plot.timecox
Plots cumulative residualsplot.cum.residuals
Plots estimates and test-processesplot.dynreg
Predictions for Survival and Competings Risks Regression for timeregpredict.aalen predict.comprisk predict.cox.aalen predict.timereg
Set up weights for delayed-entry competing risks data for comp.risk functionprep.comp.risk
Prints callprint.aalen print.comprisk print.cox.aalen print.cum.residuals print.dynreg print.prop.excess print.timecox
Identifies the multiplicative terms in Cox-Aalen model and proportional excess risk modelprop
Fits Proportional excess hazards modelprop.excess
Fit Semiparametric Proportional 0dds Modelprop.odds
Fit Semiparametric Proportional 0dds Model for the competing risks subdistributionprop.odds.subdist
For internal useaalen.des aalen.des2 aalenBase aalenBaseC additive.compSs check.missing cluster.index.timereg coef.aalen coef.comprisk coef.comprisk.ipw coef.cox.aalen coef.cox.marg coef.dynreg coef.resmean coef.timecox coef.two.stage coefBase coefcox comprisk.ipw cox.aalenBase cox.marg Cpred Csmooth2B CsmoothB des.aalen dynregBase faster.reshape is.diag kernel kmplot localTimeReg nameestimate namematrix names2formula pava percen plot.comprisk plot.cox.aalen2 plot.cums plot.predict plot.predict.comprisk plot.predict.timereg plot.resmean plot.restricted.residual.mean plot.two.stage plotConfregion plotScore pred.cum pred.des pred.stratKM predict.two.stage predictpropodds prep.glm.comprisk print.comprisk.ipw print.cox.marg print.pe.sasieni print.predict.timereg print.resmean print.two.stage prop.excessBase prop.odds.gam prop.odds.subdist.ipw pval read-design read.design read.surv residualsTimereg risk.index rm.missing semiaalen semicox semiregBase sindex.prodlim slaaop summary.comprisk summary.comprisk.ipw summary.cox.marg summary.pe.sasieni summary.predict.timereg summary.resmean summary.restricted.residual.mean summary.two.stage timecoxBase timereg.formula timetest twin.clustertrunc vcov.aalen vcov.comp.risk vcov.cox.aalen vcov.two.stage
Cut a variableqcut
Estimates marginal mean of recurrent events based on two cox modelsrecurrent.marginal.coxmean
Estimates marginal mean of recurrent eventsrecurrent.marginal.mean
Residual mean life (restricted)res.mean
Estimates restricted residual mean for Cox or Aalen modelrestricted.residual.mean
Prints summary statisticssummary.aalen summary.cox.aalen summary.dynreg summary.prop.excess summary.timecox
Prints summary statistics for goodness-of-fit tests based on cumulative residualssummary.cum.residuals
Fit Cox model with partly timevarying effects.timecox
The TRACE study group of myocardial infarctionsTRACE TRACE tTRACE
Fit Clayton-Oakes-Glidden Two-Stage modeltwo.stage
Makes wald testwald.test