Converts multi-state data back and forth between etm and msdata formats. Covariates have to be dealt with separately.
etm2msdata(etmdata, id, tra, covs)
| etmdata | Multi-state data in |
|---|---|
| id | Column name identifying the subject id |
| tra | Transition matrix in |
| covs | Vector of column names containing covariates to be included |
msdata2etm will convert from msdata format to etm
format; etm2msdata will convert from etm format to
msdata format. Both msdata2etm and etm2msdata work with
basic time-fixed covariates. Time-dependent covariates are not supported.
The function msdata2etm will work for transition-specific covariates,
but the result does not really make much sense when used in etm.
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 (T&G) tg <- data.frame(id=1:6,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, id="id") # Same thing in etm format tra <- trans2tra(tmat) tgetm <- msdata2etm(tglong, id="id") tgetm <- msdata2etm(tglong, id="id", covs=c("x1", "x2")) # with covariates # And back etm2msdata(tgetm, id="id", tra=tra)#> An object of class 'msdata' #> #> Data: #> id from to trans Tstart Tstop time status #> 1 1 1 2 1 0 1 1 1 #> 2 1 1 3 2 0 1 1 0 #> 3 1 2 3 3 1 5 4 1 #> 4 2 1 2 1 0 1 1 0 #> 5 2 1 3 2 0 1 1 1 #> 6 3 1 2 1 0 6 6 1 #> 7 3 1 3 2 0 6 6 0 #> 8 3 2 3 3 6 9 3 1 #> 9 4 1 2 1 0 6 6 1 #> 10 4 1 3 2 0 6 6 0 #> 11 4 2 3 3 6 7 1 1 #> 12 5 1 2 1 0 8 8 0 #> 13 5 1 3 2 0 8 8 1 #> 14 6 1 2 1 0 9 9 1 #> 15 6 1 3 2 0 9 9 0 #> 16 6 2 3 3 9 12 3 1#> An object of class 'msdata' #> #> Data: #> id from to trans Tstart Tstop time status x1 x2 #> 1 1 1 2 1 0 1 1 1 1 6 #> 2 1 1 3 2 0 1 1 0 1 6 #> 3 1 2 3 3 1 5 4 1 1 6 #> 4 2 1 2 1 0 1 1 0 1 5 #> 5 2 1 3 2 0 1 1 1 1 5 #> 6 3 1 2 1 0 6 6 1 1 4 #> 7 3 1 3 2 0 6 6 0 1 4 #> 8 3 2 3 3 6 9 3 1 1 4 #> 9 4 1 2 1 0 6 6 1 0 3 #> 10 4 1 3 2 0 6 6 0 0 3 #> 11 4 2 3 3 6 7 1 1 0 3 #> 12 5 1 2 1 0 8 8 0 0 2 #> 13 5 1 3 2 0 8 8 1 0 2 #> 14 6 1 2 1 0 9 9 1 0 1 #> 15 6 1 3 2 0 9 9 0 0 1 #> 16 6 2 3 3 9 12 3 1 0 1