R: Summary method for an msfit object

summary.msfit {mstate} | R Documentation

## Summary method for an msfit object

### Description

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.

### Usage

    ## S3 method for class 'msfit'
    summary(
      object,
      times,
      transitions,
      variance = TRUE,
      conf.int = 0.95,
      conf.type = c("log", "none", "plain"),
      extend = FALSE,
      ...
    )

### Arguments

`object` | Object of class 'msfit', containing estimated cumulative transition intensities for all transitions in a multi-state model
`times` | Time points at which to evaluate the cumulative transition hazards
`transitions` | The transition for which to summarize the cumulative transition hazards
`variance` | Whether or not the standard errors of the estimated cumulative transition intensities should be printed; default is `TRUE`
`conf.int` | The proportion to be covered by the confidence intervals, default is 0.95
`conf.type` | The type of confidence interval, one of "log", "none", or "plain". Defaults to "log"
`extend` | logical value: if `TRUE`, prints information for all specified times, even if there are no subjects left at the end of the specified times. This is only valid if the times argument is present
`...` | Further arguments to summary

### Value

Function `summary.msfit` returns an object of class "summary.msfit", which is a list (for each `from` state) of cumulative transition hazaards at the specified (or all) time points. The `print` method of a `summary.probtrans` doesn't return a value.

### Author(s)

Hein Putter H.Putter@lumc.nl

### See Also

`msfit`

### Examples

    # Start with example from msfit
    tmat <- trans.illdeath()
    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))
    tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"),
                     data=tg,keep=c("x1","x2"),trans=tmat)
    tglong <- expand.covs(tglong,c("x1","x2"))
    cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans),
                data=tglong,method="breslow")
    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)

    # Default, all transitions, with SE
    summary(msf)
    summary(msf, conf.type="plain")
    # Only transitions 1 and 3
    summary(msf, tra=c(1, 3))
    # Default is 95% confidence interval, change here to 90%
    summary(msf, conf.int=0.90)
    # Do not show variances (nor confidence intervals)
    summary(msf, variance=FALSE)
    # Cumulative hazards only at specified time points
    summary(msf, times=seq(0, 15, by=3))
    # Last specified time point is larger than last observed, not printed
    # Use extend=TRUE as in summary.survfit
    summary(msf, times=seq(0, 15, by=3), extend=TRUE)
    # Different types of confidence intervals, default is log
    summary(msf, times=seq(0, 15, by=3), conf.type="plain")
    summary(msf, times=seq(0, 15, by=3), conf.type="no")
    # When the number of time points specified is larger than 12, head and tail is shown
    x <- summary(msf, times=seq(5, 8, by=0.25))
    x

[Package mstate version 0.3.2 Index]