mstate (version 0.3.3)

LMAJ: Landmark Aalen-Johansen method

Description

This function implements the landmark Aalen-Johansen method of Putter & Spitoni (2016) for non-parametric estimation of transition probabilities in non-Markov models.

Usage

LMAJ(msdata, s, from, method = c("aalen", "greenwood"))

Value

A data frame containing estimates and associated standard errors of the transition probabilities P(X(t)=k | X(s) in from) with s

and from the arguments of the function.

Arguments

msdata

An "msdata" object, as for instance prepared by link{msprep}

s

The prediction time point s from which transition probabilities are to be obtained

from

Either a single state or a set of states in the state space 1,...,S

method

The method for calculating variances, as in probtrans

Author

Hein Putter

Edouard F. Bonneville

References

H. Putter and C. Spitoni (2016). Estimators of transition probabilities in non-Markov multi-state models. Submitted.

Examples

data(prothr)
tmat <- attr(prothr, "trans")
pr0 <- subset(prothr, treat=="Placebo")
attr(pr0, "trans") <- tmat
pr1 <- subset(prothr, treat=="Prednisone")
attr(pr1, "trans") <- tmat
c0 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr0)
c1 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr1)
msf0 <- msfit(c0, trans=tmat)
msf1 <- msfit(c1, trans=tmat)
# Comparison as in Figure 2 of Titman (2015)
# Aalen-Johansen
pt0 <- probtrans(msf0, predt=1000)[[2]]
pt1 <- probtrans(msf1, predt=1000)[[2]]
par(mfrow=c(1,2))
plot(pt0$time, pt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61),
     xlab="Time since randomisation (days)", ylab="Probability")
lines(pt1$time, pt1$pstate1, type="s", lwd=2, lty=3)
legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n")
title(main="Aalen-Johansen")
# Landmark Aalen-Johansen
LMpt0 <- LMAJ(msdata=pr0, s=1000, from=2)
LMpt1 <- LMAJ(msdata=pr1, s=1000, from=2)
plot(LMpt0$time, LMpt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61),
     xlab="Time since randomisation (days)", ylab="Probability")
lines(LMpt1$time, LMpt1$pstate1, type="s", lwd=2, lty=3)
legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n")
title(main="Landmark Aalen-Johansen")