R: Summary method for a probtrans object

summary.probtrans {mstate} | R Documentation

## Summary method for a probtrans object

### Description

Summary method for an object of class 'probtrans'. It prints a selection of the estimated transition probabilities, and, if requested, also of the variances.

### Usage

    ## S3 method for class 'probtrans'
    summary(object,from,complete=FALSE,variance=TRUE,...)

### Arguments

`object` | Object of class 'probtrans', containing estimated transition probabilities from and to all states in a multi-state model
`from` | Specifies from which state the transition probabilities are to be printed. Should be subset of 1:S, with S the number of states in the multi-state model. If missing, transition probabilities are printed from all starting states
`complete` | Whether or not the complete estimated transition probabilities should be printed (`TRUE`) or not (`FALSE`); default is `FALSE`, in which case the estimated transition probilities will be printed for the first and last 6 time points of each starting state (or all when there are at most 12 of these time points
`variance` | Whether or not the standard errors of the estimated transition probabilities should be printed; default is `TRUE`
`...` | Further arguments to summary

### Value

No return value

### Author(s)

Hein Putter H.Putter@lumc.nl

### See Also

`probtrans`

### Examples

    # 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)
    # probtrans
    pt <- probtrans(msf,predt=0)
    # default summary
    summary(pt)
    # summary without standard errors
    summary(pt,variance=FALSE)

[Package mstate version 0.2.12 Index]