summary.msfit {mstate} | R Documentation |
Summary method for an object of class 'msfit'. It prints a selection of the estimated cumulative transition intensities, and, if requested, also of the (co)variances.
## S3 method for class 'msfit' summary(object,complete=FALSE,variance=FALSE,...)
object |
Object of class 'msfit', containing estimated cumulative transition intensities for all transitions in a multi-state model |
complete |
Whether or not the complete estimated cumulative
transition intensities should be printed ( |
variance |
Whether or not the (co)variances of the estimated
cumulative transition intensities should be printed; default is
|
... |
Further arguments to summary |
No return value
Hein Putter H.Putter@lumc.nl
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) print(msf) # standard summary summary(msf) # including variances and covariances summary(msf,variance=TRUE)