R: Compute subject-specific transition hazards with...

msfit {mstate} | R Documentation

## Compute subject-specific transition hazards with (co-)variances

### Description

This function computes subject-specific or overall cumulative transition hazards for each of the possible transitions in the multi-state model. If requested, also the variances and covariances of the estimated cumulative transition hazards are calculated.

### Usage

    msfit(object, newdata, variance=TRUE, vartype=c("aalen","greenwood"), trans)

### Arguments

`object` | A `coxph` object describing the fit of the multi-state model
`newdata` | A data frame with the same variable names as those that appear in the `coxph` formula. Its use is somewhat different from `survfit`. See Details. The argument `newdata` may be omitted only if the right hand side of the formula in the `coxph` object is `~strata(trans)`
`variance` | A logical value indicating whether the (co-)variances of the subject-specific transition hazards should be computed. Default is `TRUE`
`vartype` | A character string specifying the type of variances to be computed (so only needed if `variance`=`TRUE`). Possible values are `"aalen"` or `"greenwood"`
`trans` | Transition matrix describing the states and transitions in the multi-state model. See `trans` in `msprep` for more detailed information

### Details

The data frame needs to have one row for each transition in the multi-state model. An additional column `strata` (numeric) is needed to describe for each transition to which stratum it belongs. The name has to be `strata`, even if in the original `coxph` call another variable was used. For details refer to de Wreede, Fiocco & Putter (2010). So far, the results have been checked only for the `"breslow"` method of dealing with ties in `coxph`, so this is recommended.

### Value

An object of class `"msfit"`, which is a list containing

`Haz` | A data frame with `time`, `Haz`, `trans`, containing the estimated subject-specific hazards for each of the transitions in the multi-state model
`varHaz` | A data frame with `time`, `Haz`, `trans1`, `trans2` containing the variances (`trans1`=`trans2`) and covariances (`trans1`<`trans2`) of the estimated hazards. This element is only returned when `variance`=`TRUE`
`trans` | The transition matrix used

### Author(s)

Hein Putter H.Putter@lumc.nl

### References

Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.

Therneau TM, Grambsch PM (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York.

de Wreede LC, Fiocco M, and Putter H (2010). The mstate package for estimation and prediction in non- and semi-parametric multi-state and competing risks models. Computer Methods and Programs in Biomedicine 99, 261–274.

de Wreede LC, Fiocco M, and Putter H (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software, Volume 38, Issue 7.

### See Also

`plot.msfit`

### 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)
    msfit(cx,newdata,trans=tmat)

[Package mstate version 0.2.12 Index]