probtrans  R Documentation 
This function computes subjectspecific or overall transition probabilities in multistate models. If requested, also standard errors are calculated.
probtrans(
object,
predt,
direction = c("forward", "fixedhorizon"),
method = c("aalen", "greenwood"),
variance = TRUE,
covariance = FALSE
)
object 
msfit object containing estimated cumulative hazards for each of the transitions in the multistate model and, if standard errors are requested, (co)variances of these cumulative hazards for each pair of transitions 
predt 
A positive number indicating the prediction time. This is
either the time at which the prediction is made (if 
direction 
One of 
method 
A character string specifying the type of variances to be
computed (so only needed if either 
variance 
Logical value indicating whether standard errors are to be
calculated (default is 
covariance 
Logical value indicating whether covariances of transition
probabilities for different states are to be calculated (default is

For details refer to de Wreede, Fiocco & Putter (2010).
An object of class "probtrans"
, which is a list of which item
[[s]] contains a data frame with the estimated transition probabilities (and
standard errors if variance
=TRUE
) from state s. If
covariance
=TRUE
, item varMatrix
contains an array of
dimension K^2 x K^2 x (nt+1) (with K the number of states and nt the
distinct transition time points); the time points correspond to those in the
data frames with the estimated transition probabilities. Finally, there are
items trans
, method
, predt
, direction
, recording
the transition matrix, and the method, predt and direction arguments used in
the call to probtrans. Plot and summary methods have been defined for
"probtrans"
objects.
Liesbeth de Wreede and Hein Putter H.Putter@lumc.nl
Andersen PK, Borgan O, Gill RD, Keiding N (1993). Statistical Models Based on Counting Processes. Springer, New York.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multistate 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 semiparametric multistate 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 MultiState Models. Journal of Statistical Software, Volume 38, Issue 7.
# transition matrix for illnessdeath 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)
HvH < msfit(cx,newdata,trans=tmat)
# probtrans
pt < probtrans(HvH,predt=0)
# predictions from state 1
pt[[1]]
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