timereg (version 1.9.3)

sim.cause.cox: Simulation of cause specific from Cox models.

Description

Simulates data that looks like fit from cause specific Cox models. Censor data automatically. When censoring is given in the list of causes this will give censoring that looks like the data. Covariates are drawn from data-set with replacement. This gives covariates like the data.

Usage

# S3 method for cause.cox
sim(coxs, n, data = NULL, cens = NULL,
  rrc = NULL, ...)

Arguments

coxs

list of cox models.

n

number of simulations.

data

to extract covariates for simulations (draws from observed covariates).

cens

specifies censoring model, if NULL then only censoring for each cause at end of last event of this type. if "is.matrix" then uses cumulative. hazard given, if "is.scalar" then uses rate for exponential, and if not given then takes average rate of in simulated data from cox model. But censoring can also be given as a cause.

rrc

possible vector of relative risk for cox-type censoring.

...

arguments for pc.hazard, for example entry-time

Examples

# NOT RUN {
nsim <- 1000
data(bmt)
cox1 <- cox.aalen(Surv(time,cause==1)~prop(tcell)+prop(platelet),data=bmt,robust=0)
cox2 <- cox.aalen(Surv(time,cause==2)~prop(tcell)+prop(platelet),data=bmt,robust=0)
coxs <- list(cox1,cox2)
dd <- sim.cause.cox(coxs,nsim,data=bmt)
scox1 <- cox.aalen(Surv(time,status==1)~prop(tcell)+prop(platelet),data=dd,robust=0)
scox2 <- cox.aalen(Surv(time,status==2)~prop(tcell)+prop(platelet),data=dd,robust=0)
### 
cbind(cox1$gamma,scox1$gamma)
cbind(cox2$gamma,scox2$gamma)
par(mfrow=c(1,2))
plot(cox1); lines(scox1$cum,col=2)
plot(cox2$cum,type="l");
lines(scox2$cum,col=2)
          
          
# }
# NOT RUN {
### do not test to avoid dependence on mets
library(mets)          
data(bmt)
cox1 <- phreg(Surv(time,cause==1)~tcell+platelet,data=bmt)
cox2 <- phreg(Surv(time,cause==2)~tcell+platelet,data=bmt)
coxs <- list(cox1,cox2)
dd <- sim.cause.cox(coxs,nsim,data=bmt)
scox1 <- phreg(Surv(time,status==1)~tcell+platelet,data=dd)
scox2 <- phreg(Surv(time,status==2)~tcell+platelet,data=dd)
cbind(cox1$coef,scox1$coef)
cbind(cox2$coef,scox2$coef)
par(mfrow=c(1,2))
basehazplot.phreg(cox1); basehazplot.phreg(scox1,add=TRUE); 
basehazplot.phreg(cox2); basehazplot.phreg(scox2,add=TRUE); 

cox1 <- phreg(Surv(time,cause==1)~strata(tcell)+platelet,data=bmt)
cox2 <- phreg(Surv(time,cause==2)~strata(tcell)+platelet,data=bmt)
coxs <- list(cox1,cox2)
dd <- sim.cause.cox(coxs,nsim,data=bmt)
scox1 <- phreg(Surv(time,status==1)~strata(tcell)+platelet,data=dd)
scox2 <- phreg(Surv(time,status==2)~strata(tcell)+platelet,data=dd)
cbind(cox1$coef,scox1$coef)
cbind(cox2$coef,scox2$coef)
par(mfrow=c(1,2))
basehazplot.phreg(cox1); basehazplot.phreg(scox1,add=TRUE); 
basehazplot.phreg(cox2); basehazplot.phreg(scox2,add=TRUE); 

# coxph          
cox1 <- coxph(Surv(time,cause==1)~tcell+platelet,data=bmt)
cox2 <- coxph(Surv(time,cause==2)~tcell+platelet,data=bmt)
coxs <- list(cox1,cox2)
dd <- sim.cause.cox(coxs,nsim,data=bmt)
scox1 <- coxph(Surv(time,status==1)~tcell+platelet,data=dd)
scox2 <- coxph(Surv(time,status==2)~tcell+platelet,data=dd)
cbind(cox1$coef,scox1$coef)
cbind(cox2$coef,scox2$coef)
# }