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,
      times,
      from = 1,
      to = 0,
      variance = TRUE,
      conf.int = 0.95,
      conf.type = c("log", "none", "plain"),
      extend = FALSE,
      ...
    )

### Arguments

`object` | Object of class 'probtrans', containing estimated transition probabilities from and to all states in a multi-state model
`times` | Time points at which to evaluate the transition probabilites
`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. Default is print from state 1 only. User can specify from=0 to print transition probabilities from all states
`to` | Specifies the transition probabilities to which state are to be printed. User can specify to=0 to print transition probabilities to all states. This is also the default
`variance` | Whether or not the standard errors of the estimated transition probabilities 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 print

### Value

Function `summary.probtrans` returns an object of class "summary.probtrans", which is a list (for each `from` state) of transition probabilities 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

`probtrans`

### Examples

    # First run the example of probtrans
    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)
    HvH <- msfit(cx,newdata,trans=tmat)
    pt <- probtrans(HvH,predt=0)

    # Default, prediction from state 1
    summary(pt)
    # Only from states 1 and 3
    summary(pt, from=c(1, 3))
    # Use from=0 for prediction from all states
    summary(pt, from=0)
    # Only to states 1 and 2
    summary(pt, to=1:2)
    # Default is 95% confidence interval, change here to 90%
    summary(pt, to=1:2, conf.int=0.90)
    # Do not show variances (nor confidence intervals)
    summary(pt, to=1:2, variance=FALSE)
    # Transition probabilities only at specified time points
    summary(pt, 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(pt, times=seq(0, 15, by=3), extend=TRUE)
    # Different types of confidence intervals, default is log
    summary(pt, times=seq(0, 15, by=3), conf.type="plain")
    summary(pt, 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(pt, times=seq(5, 8, by=0.25))
    x

[Package mstate version 0.3.1 Index]