summary.probtrans.subjects {icmstate} | R Documentation |
Summary method for a probtrans.subjects object
Description
Summary method for an object of class 'probtrans.subjects'. It prints a selection of
the estimated transition probabilities. Wrapper for
summary.probtrans
.
Usage
## S3 method for class 'probtrans.subjects'
summary(object, id, times, from = 1, to = 0, extend = FALSE, ...)
Arguments
object |
Object of class 'probtrans.subjects', containing estimated transition probabilities from and to all states in a multi-state model |
id |
Subject identifier |
times |
Time points at which to evaluate the transition probabilites |
from |
Specifies from which state the transition probabilities are to be printed. Should be subset of 1:S, with S the number of states in the multi-state model. Default is print from state 1 only. User can specify from=0 to print transition probabilities from all states |
to |
Specifies the transition probabilities to which state are to be printed. User can specify to=0 to print transition probabilities to all states. This is also the default |
extend |
logical value: if |
... |
Further arguments to |
Value
Function summary.probtrans
returns an object of class
"summary.probtrans.subjects", which is a list (for each from
state) of
transition probabilities at the specified (or all) time points. The
print
method of a summary.probtrans.subjects
doesn't return a value.
Author(s)
Hein Putter and Daniel Gomon
See Also
Examples
if(require("mstate")){
data(ebmt3)
n <- nrow(ebmt3)
tmat <- transMat(x = list(c(2, 3), c(3), c()), names = c("Tx",
"PR", "RelDeath"))
ebmt3$prtime <- ebmt3$prtime/365.25
ebmt3$rfstime <- ebmt3$rfstime/365.25
covs <- c("dissub", "age", "drmatch", "tcd", "prtime")
msbmt <- msprep(time = c(NA, "prtime", "rfstime"), status = c(NA,
"prstat", "rfsstat"), data = ebmt3, trans = tmat, keep = covs)
#Expand covariates so that we can have transition specific covariates
msbmt <- expand.covs(msbmt, covs, append = TRUE, longnames = FALSE)
#Simple model, transition specific covariates, each transition own baseline hazard
c1 <- coxph(Surv(Tstart, Tstop, status) ~ dissub1.1 + dissub2.1 +
age1.1 + age2.1 + drmatch.1 + tcd.1 + dissub1.2 + dissub2.2 +
age1.2 + age2.2 + drmatch.2 + tcd.2 + dissub1.3 + dissub2.3 +
age1.3 + age2.3 + drmatch.3 + tcd.3 + strata(trans), data = msbmt,
method = "breslow")
#We need to make a data.frame containing all subjects of interest
ttmat <- to.trans2(tmat)[, c(2, 3, 1)]
names(ttmat)[3] <- "trans"
nd_n <- NULL
for (j in 1:30) {
# Select global covariates of subject j
cllj <- ebmt3[j, covs]
nd2 <- cbind(ttmat, rep(j, 3), rbind(cllj, cllj, cllj))
colnames(nd2)[4] <- "id"
# Make nd2 of class msdata to use expand.covs
attr(nd2, "trans") <- tmat
class(nd2) <- c("msdata", "data.frame")
nd2 <- expand.covs(nd2, covs=covs, longnames = FALSE)
nd_n <- rbind(nd_n, nd2)
}
icmstate_pt <- probtrans_coxph(c1, predt = 0, direction = "forward",
newdata = nd_n, trans = tmat)
#Obtain summary of probtrans.subjects object
plot(icmstate_pt, id = 2)
}