Converts multi-state data back and forth between etm and msdata formats. Covariates have to be dealt with separately.
Details
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.
Author
Hein Putter H.Putter@lumc.nl
Examples
# 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
etm2msdata(tgetm, id="id", tra=tra, covs=c("x1", "x2")) # with covariates
#> 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