# Flexible Regression Models for Survival Data

## Documentation for package ‘timereg’ version 1.9.4

- DESCRIPTION file.

## Help Pages

A B C D E F G I K L M N P Q R S T V W misc

## -- A --

aalen | Fit additive hazards model
aalen.des | For internal use
aalen.des2 | For internal use
aalenBase | For internal use
aalenBaseC | For internal use
addCums | Simulation of Piecewise constant hazard model (Cox).
additive.compSs | For internal use
as.character.Event | Event history object
as.matrix.Event | Event history object

## -- B --

bmt | The Bone Marrow Transplant Data

## -- C --

cause.pchazard.sim | Simulation of Piecewise constant hazard models with two causes (Cox).
cd4 | The multicenter AIDS cohort study
check.missing | For internal use
cluster.index.timereg | For internal use
coef.aalen | For internal use
coef.comprisk | For internal use
coef.comprisk.ipw | For internal use
coef.cox.aalen | For internal use
coef.cox.ipw | Missing data IPW Cox
coef.cox.marg | For internal use
coef.dynreg | For internal use
coef.resmean | For internal use
coef.timecox | For internal use
coef.two.stage | For internal use
coefBase | For internal use
coefcox | For internal use
comp.risk | Competings Risks Regression
comprisk.ipw | For internal use
const | Identifies parametric terms of model
cox | Identifies proportional excess terms of model
cox.aalen | Fit Cox-Aalen survival model
cox.aalenBase | For internal use
cox.ipw | Missing data IPW Cox
cox.marg | For internal use
Cpred | For internal use
csl | CSL liver chirrosis data
Csmooth2B | For internal use
CsmoothB | For internal use
cum.residuals | Model validation based on cumulative residuals
cumh=cbind(breaks,cumhazard) | Simulation of Piecewise constant hazard models with two causes (Cox).
cumh=cbind(breaks,rates), | Simulation of Piecewise constant hazard models with two causes (Cox).
cumh=FALSE | Simulation of Piecewise constant hazard models with two causes (Cox).
cumh=TRUE | Simulation of Piecewise constant hazard models with two causes (Cox).

## -- D --

des.aalen | For internal use
diabetes | The Diabetic Retinopathy Data
dynreg | Fit time-varying regression model
dynregBase | For internal use

## -- E --

Event | Event history object
event.split | EventSplit (SurvSplit).

## -- F --

faster.reshape | For internal use
first | Simulation of Piecewise constant hazard models with two causes (Cox).
format.Event | Event history object

## -- G --

Gprop.odds | Fit Generalized Semiparametric Proportional 0dds Model

## -- I --

if | Simulation of Piecewise constant hazard models with two causes (Cox).
invsubdist | Finds inverse of piecwise linear sub-distribution
is | Simulation of Piecewise constant hazard models with two causes (Cox).
is.diag | For internal use

## -- K --

kernel | For internal use
kmplot | For internal use
krylow.pls | Fits Krylow based PLS for additive hazards model

## -- L --

localTimeReg | For internal use

## -- M --

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

## -- N --

nameestimate | For internal use
namematrix | For internal use
names2formula | For internal use

## -- P --

pava | For internal use
pava.pred | Make predictions of predict functions in rows mononotone
pc.hazard | Simulation of Piecewise constant hazard model (Cox).
pe.sasieni | Fits Proportional excess hazards model with fixed offsets
percen | For internal use
plot.aalen | Plots estimates and test-processes
plot.comprisk | For internal use
plot.cox.aalen | Plots estimates and test-processes
plot.cox.aalen2 | For internal use
plot.cum.residuals | Plots cumulative residuals
plot.cums | For internal use
plot.dynreg | Plots estimates and test-processes
plot.predict | For internal use
plot.predict.comprisk | For internal use
plot.predict.timereg | For internal use
plot.prop.excess | Plots estimates and test-processes
plot.resmean | For internal use
plot.restricted.residual.mean | For internal use
plot.timecox | Plots estimates and test-processes
plot.two.stage | For internal use
plotConfregion | For internal use
plotScore | For internal use
pre.cifs | Simulation of output from Cumulative incidence regression model
pred.cum | For internal use
pred.des | For internal use
pred.stratKM | For internal use
predict.aalen | Predictions for Survival and Competings Risks Regression for timereg
predict.comprisk | Predictions for Survival and Competings Risks Regression for timereg
predict.cox.aalen | Predictions for Survival and Competings Risks Regression for timereg
predict.timereg | Predictions for Survival and Competings Risks Regression for timereg
predict.two.stage | For internal use
predictpropodds | For internal use
prep.comp.risk | Set up weights for delayed-entry competing risks data for comp.risk function
prep.glm.comprisk | For internal use
print.aalen | Prints call
print.comprisk | Prints call
print.comprisk.ipw | For internal use
print.cox.aalen | Prints call
print.cox.ipw | Missing data IPW Cox
print.cox.marg | For internal use
print.cum.residuals | Prints call
print.dynreg | Prints call
print.Event | Event history object
print.pe.sasieni | For internal use
print.predict.timereg | For internal use
print.prop.excess | Prints call
print.resmean | For internal use
print.timecox | Prints call
print.two.stage | For internal use
prop | Identifies the multiplicative terms in Cox-Aalen model and proportional excess risk model
prop.excess | Fits Proportional excess hazards model
prop.excessBase | For internal use
prop.odds | Fit Semiparametric Proportional 0dds Model
prop.odds.gam | For internal use
prop.odds.subdist | Fit Semiparametric Proportional 0dds Model for the competing risks subdistribution
prop.odds.subdist.ipw | For internal use
pval | For internal use

## -- Q --

qcut | Cut a variable

## -- R --

rate | Simulation of Piecewise constant hazard models with two causes (Cox).
rbind.Event | Event history object
rchaz | Simulation of Piecewise constant hazard model (Cox).
rcrisk | Simulation of Piecewise constant hazard models with two causes (Cox).
read-design | For internal use
read.design | For internal use
read.fit | Simulation of output from Cox model.
read.surv | For internal use
recurrent.marginal.coxmean | Estimates marginal mean of recurrent events based on two cox models
recurrent.marginal.mean | Estimates marginal mean of recurrent events
res.mean | Residual mean life (restricted)
residualsTimereg | For internal use
restricted.residual.mean | Estimates restricted residual mean for Cox or Aalen model
risk.index | For internal use
rm.missing | For internal use

## -- S --

semiaalen | For internal use
semicox | For internal use
semiregBase | For internal use
sim.cause.cox | Simulation of cause specific from Cox models.
sim.cif | Simulation of output from Cumulative incidence regression model
sim.cifs | Simulation of output from Cumulative incidence regression model
sim.cox | Simulation of output from Cox model.
simrchaz | Simulation of Piecewise constant hazard model (Cox).
simsubdist | Simulation from subdistribution function assuming piecwise linearity
sindex.prodlim | For internal use
slaaop | For internal use
sTRACE | The TRACE study group of myocardial infarction
subdist | Simulation of output from Cumulative incidence regression model
summary.aalen | Prints summary statistics
summary.comprisk | For internal use
summary.comprisk.ipw | For internal use
summary.cox.aalen | Prints summary statistics
summary.cox.ipw | Missing data IPW Cox
summary.cox.marg | For internal use
summary.cum.residuals | Prints summary statistics for goodness-of-fit tests based on cumulative residuals
summary.dynreg | Prints summary statistics
summary.Event | Event history object
summary.pe-sasieni | Fits Proportional excess hazards model with fixed offsets
summary.pe.sasieni | For internal use
summary.predict.timereg | For internal use
summary.prop.excess | Prints summary statistics
summary.resmean | For internal use
summary.restricted.residual.mean | For internal use
summary.timecox | Prints summary statistics
summary.two.stage | For internal use

## -- T --

timecox | Fit Cox model with partly timevarying effects.
timecoxBase | For internal use
timereg.formula | For internal use
timetest | For internal use
TRACE | The TRACE study group of myocardial infarction
tTRACE | The TRACE study group of myocardial infarction
twin.clustertrunc | For internal use
two.stage | Fit Clayton-Oakes-Glidden Two-Stage model

## -- V --

vcov.aalen | For internal use
vcov.comp.risk | For internal use
vcov.cox.aalen | For internal use
vcov.two.stage | For internal use

## -- W --

wald.test | Makes wald test

## -- misc --

## | Simulation of Piecewise constant hazard models with two causes (Cox).
0 | Simulation of Piecewise constant hazard models with two causes (Cox).
[.Event | Event history object