Create a data structures suitable for use with packages mstate or etm.
The mstate package requires input in the form of a stacked
dataset with specific variable names. This is provided by
msdata.Lexis. The resulting dataframe contains the same
information as the result of a call to stack.Lexis.
The etm package requires input (almost) in the form of a
Lexis object, but with specific column names etc. This is
provided by etm.Lexis.
msdata(obj, ...)
## S3 method for class 'Lexis'
msdata(obj,
time.scale = timeScales(obj)[1],
... )
## S3 method for class 'Lexis'
etm( data,
time.scale = timeScales(data)[1],
cens.name = "cens",
s = 0,
t = "last",
covariance = TRUE,
delta.na = TRUE,
... )obj |
A |
data |
A |
time.scale |
Name or number of timescale in the |
cens.name |
Name of the code for censoring used by |
s |
Passed on to |
t |
Passed on to |
covariance |
Passed on to |
delta.na |
Passed on to |
... |
Further arguments. |
msdata.Lexis returns a dataframe with the Lexis specific
variables stripped, and with the following added: id,
Tstart, Tstop, from, to, trans,
status, which are used in the mstate package.
etm.Lexis transforms the Lexis object into a dataframe
suitable for analysis by the function etm from the etm
package, and actually calls this function, so returns an object of
class etm.
Bendix Carstensen, b@bxc.dk, http://bendixcarstensen.com
data(DMlate)
str(DMlate)
dml <- Lexis( entry = list(Per=dodm,Age=dodm-dobth,DMdur=0),
exit = list(Per=dox),
exit.status = factor(!is.na(dodth),labels=c("DM","Dead")),
data = DMlate[1:1000,] )
dmi <- cutLexis( dml, cut=dml$doins, new.state="Ins", pre="DM" )
summary( dmi )
# Use the interface to the mstate package
if( require(mstate) )
{
ms.dmi <- msdata.Lexis( dmi )
# Check that all the transitions and person-years got across.
with( ms.dmi, rbind( table(status,trans),
tapply(Tstop-Tstart,trans,sum) ) )
}
# Use the etm package directly with a Lexis object
if( require(etm) )
{
dmi <- subset(dmi,lex.id<1000)
etm.D <- etm.Lexis( dmi, time.scale=3 )
str( etm.D )
plot( etm.D, col=rainbow(5), lwd=2, lty=1, xlab="DM duration" )
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