plot.msfit.subjects: Plot method for an msfit.subjects object

In hputter/mstate: Data Preparation, Estimation and Prediction in Multi-State Models

Plot method for an msfit.subjects object

Description

Plot method for an object of class "msfit.subjects". It plots the estimated cumulative transition intensities in the multi-state model for a single subject. Wrapper for plot.msfit.

Usage

## S3 method for class 'msfit.subjects'
plot(x, id, ...)

Arguments

x	Object of class "msfit.subjects", containing estimated transition intensity matrices for all transitions in a multi-state model for (multiple) subjects
id	Identifier of subject to make plot for.
...	Further arguments to plot.msfit

Value

No return value

Author(s)

Hein Putter [e-mail]

Edouard F. Bonneville [e-mail]

Daniel Gomon

See Also

msfit_subjects

Examples

# transition matrix for illness-death 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)
#Fit on multiple subjects at once, by providing 'id' column.
#cx was fit using strata(trans), so we must have a 'trans' column.
newdata <- data.frame(id=rep(1:3, each = 3),x1.1=c(0,0,0,1,0,1,0,1,0),
                      x2.2=c(0,1,0,0,0,0,1,0,1), trans = rep(1:3, 3))
msf_subj <- msfit_subjects(cx,newdata,trans=tmat)
# standard plot for subject 1
plot(msf_subj,id = 1)
# standard plot for subject 2
plot(msf_subj,id = 2)
# specifying line width, color, and legend
plot(msf_subj,id = 1,lwd=2,col=c("darkgreen","darkblue","darkred"),legend=c("1->2","1->3","2->3"))
# separate plots for each transition
par(mfrow=c(2,2))
plot(msf_subj, id = 1, type="separate",lwd=2)
par(mfrow=c(1,1))

hputter/mstate documentation built on July 17, 2025, 2:04 a.m.