plot.prodlim {prodlim} | R Documentation |
Function to plot survival and cumulative incidence curves against time.
## S3 method for class 'prodlim': plot(x, what, cause = 1, newdata, add = FALSE, col, lty, lwd, ylim, xlim, xlab = "Time", ylab, legend = TRUE, legend.args= NULL, mark.time = FALSE, cex.mark.time = 1.5, conf.int = TRUE, conf.int.args = list(col = "gray"), atrisk, atrisk.args, timeOrigin,...)
x |
an object of class `prodlim' as returned by the
prodlim function. |
what |
controls what part of the object is plotted.
Defaults to "survival" for the Kaplan-Meier estimate of
the survival function in two state models and to
"incidence" for the Aalen-Johansen estimate of the
cumulative incidence function in competing risk models |
cause |
Determines the cause of the cumulative incidence function. When there are strata defined by newdata only one cause is possible. |
newdata |
a data frame containing strata for which plotted curves are desired. |
add |
if 'TRUE' curves are added to an existing plot. |
col |
color for curves defaults to 1:number(curves) |
lty |
line type for curves defaults to 1 |
lwd |
line width for all curves |
ylim |
limits of the y-axis |
xlim |
limits of the x-axis |
ylab |
label for the y-axis |
xlab |
label for the x-axis |
legend |
if TRUE a legend is be plotted automatically |
legend.args |
list of arguments that is passed to the function legend |
mark.time |
if TRUE the curves are tick-marked at right censoring times |
cex.mark.time |
cex for the tick-marks if mark.time is set TRUE |
conf.int |
if TRUE pointwise confidence intervals are plotted |
conf.int.args |
list with extra arguments like col, lty, etc. used for the
pointwise confidence intervals. Extra argument time
determines time points at which confidence intervals are plotted. |
atrisk |
if TRUE display numbers of subjects at risk. if data are cluster correlated also the number of clusters with at least one subject at risk is given. |
atrisk.args |
list of extra arguments for plotting of the numbers
at risk. Recognized extra arguments are: times : at which time
points numbers are plotted. labels vector of labels,
e.g. "No. Patients". |
timeOrigin |
Start of the time axis |
... |
graphical parameters that are passed to function plot |
See examples.
NULL
Similar functionality is provided by the function
plot.survfit
of the survival library
Thomas Alexander Gerds <tag@biostat.ku.dk>
prodlim
,plot.Hist
,summary.prodlim
,
neighborhood
## simulate right censored data from a two state model dat <- data.frame(time=rexp(100),status=rbinom(100,1,.3),X=rbinom(100,1,.5),Z=rnorm(100,10,3),patnr=sample(1:10,size=100,replace=TRUE)) with(dat,plot(Hist(time,status))) ### marginal Kaplan-Meier estimator kmfit <- prodlim(Hist(time, status) ~ 1, data = dat) plot(kmfit) ### Kaplan-Meier in discrete strata kmfitX <- prodlim(Hist(time, status) ~ X, data = dat) plot(kmfitX) ### Kaplan-Meier in continuous strata kmfitZ <- prodlim(Hist(time, status) ~ Z, data = dat) plot(kmfitZ,newdata=data.frame(Z=c(5,7,12))) ### Cluster-correlated data kmfitC <- prodlim(Hist(time, status) ~ cluster(patnr), data = dat) plot(kmfitC,atrisk.args=list(labels=c("Units","Patients"))) ## simulate right censored data from a competing risk model datCR <- data.frame(time=rexp(100),status=rbinom(100,2,.3),X=rbinom(100,1,.5),Z=rnorm(100,10,3)) with(datCR,plot(Hist(time,status))) ### marginal Aalen-Johansen estimator ajfit <- prodlim(Hist(time, status) ~ 1, data = datCR) plot(ajfit) ### conditional Aalen-Johansen estimator ajfitXZ <- prodlim(Hist(time, status) ~ X+Z, data = datCR) plot(ajfitXZ,newdata=data.frame(X=c(1,1,0),Z=c(4,10,10))) plot(ajfitXZ,newdata=data.frame(X=c(1,1,0),Z=c(4,10,10)),cause=2)