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:
timereg_2.0.6.tar.gz
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timereg.pdf |timereg.html✨
timereg/json (API)
| # Install 'timereg' in R: |
| install.packages('timereg', repos = c('https://scheike.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/scheike/timereg/issues
- 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
Last updated 3 months agofrom:53fe9a56f0. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win-x86_64 | OK | Nov 05 2024 |
| R-4.5-linux-x86_64 | OK | Nov 05 2024 |
| R-4.4-win-x86_64 | OK | Nov 05 2024 |
| R-4.4-mac-x86_64 | OK | Nov 05 2024 |
| R-4.4-mac-aarch64 | OK | Nov 05 2024 |
| R-4.3-win-x86_64 | OK | Nov 05 2024 |
| R-4.3-mac-x86_64 | OK | Nov 05 2024 |
| R-4.3-mac-aarch64 | OK | Nov 05 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 page | Topics |
|---|---|
| Fit additive hazards model | aalen |
| The Bone Marrow Transplant Data | bmt |
| The multicenter AIDS cohort study | cd4 |
| Competings Risks Regression | comp.risk |
| Identifies parametric terms of model | const |
| Identifies proportional excess terms of model | cox |
| Fit Cox-Aalen survival model | cox.aalen |
| Missing data IPW Cox | coef.cox.ipw cox.ipw print.cox.ipw summary.cox.ipw |
| CSL liver chirrosis data | csl |
| Model validation based on cumulative residuals | cum.residuals |
| The Diabetic Retinopathy Data | diabetes |
| Fit time-varying regression model | dynreg |
| Event history object | as.character.Event as.matrix.Event Event format.Event print.Event rbind.Event summary.Event [.Event |
| EventSplit (SurvSplit). | event.split |
| Fit Generalized Semiparametric Proportional 0dds Model | Gprop.odds |
| Fits Krylow based PLS for additive hazards model | krylow.pls |
| Melanoma data and Danish population mortality by age and sex | mela.pop |
| The Melanoma Survival Data | melanoma |
| my version of the PBC data of the survival package | mypbc |
| Make predictions of predict functions in rows mononotone | pava.pred |
| Fits Proportional excess hazards model with fixed offsets | pe.sasieni summary.pe-sasieni |
| Plots estimates and test-processes | plot.aalen plot.cox.aalen plot.prop.excess plot.timecox |
| Plots cumulative residuals | plot.cum.residuals |
| Plots estimates and test-processes | plot.dynreg |
| Predictions for Survival and Competings Risks Regression for timereg | predict.aalen predict.comprisk predict.cox.aalen predict.timereg |
| Set up weights for delayed-entry competing risks data for comp.risk function | prep.comp.risk |
| Prints call | print.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 model | prop |
| Fits Proportional excess hazards model | prop.excess |
| Fit Semiparametric Proportional 0dds Model | prop.odds |
| Fit Semiparametric Proportional 0dds Model for the competing risks subdistribution | prop.odds.subdist |
| For internal use | aalen.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 variable | qcut |
| Estimates marginal mean of recurrent events based on two cox models | recurrent.marginal.coxmean |
| Estimates marginal mean of recurrent events | recurrent.marginal.mean |
| Residual mean life (restricted) | res.mean |
| Estimates restricted residual mean for Cox or Aalen model | restricted.residual.mean |
| Prints summary statistics | summary.aalen summary.cox.aalen summary.dynreg summary.prop.excess summary.timecox |
| Prints summary statistics for goodness-of-fit tests based on cumulative residuals | summary.cum.residuals |
| Fit Cox model with partly timevarying effects. | timecox |
| The TRACE study group of myocardial infarction | sTRACE TRACE tTRACE |
| Fit Clayton-Oakes-Glidden Two-Stage model | two.stage |
| Makes wald test | wald.test |
