https://github.com/cran/rstpm2
Tip revision: 13e45eaa4f4a7f231224f1b8ca4dff03903d250b authored by Mark Clements on 31 August 2017, 20:37:09 UTC
version 1.4.0
version 1.4.0
Tip revision: 13e45ea
plot-methods.Rd
\name{plot-methods}
\docType{methods}
\alias{plot-methods}
\alias{plot,stpm2-method}
\title{ plots for an stpm2 fit}
\description{
Given an \code{stpm2} fit, return a plot
}
\section{Methods}{
\describe{
\item{x = "stpm2", y = "missing"}{an \code{stpm2} fit}
}}
\usage{
\S4method{plot}{stpm2}(x,y,newdata,type="surv",
xlab="Time",line.col=1,ci.col="grey",
add=FALSE,ci=TRUE,rug=TRUE,
var=NULL,...)
}
\arguments{
\item{x}{an \code{stpm2} object}
\item{y}{not used (for generic compatibility)}
\item{newdata}{required list of new data. This defines the unexposed
newdata (\emph{excluding} the event times).}
\item{type}{specify the type of prediction:
\itemize{
\item{"surv"}{survival probabilities}
\item{"cumhaz"}{cumulative hazard}
\item{"hazard"}{hazard}
\item{"hr"}{hazard ratio}
\item{"sdiff"}{survival difference}
\item{"hdiff"}{hazard difference}
}
}
\item{xlab}{x-axis label}
\item{line.col}{line colour}
\item{ci.col}{confidence interval colour}
\item{ci}{whether to plot the confidence interval band (default=TRUE)}
\item{add}{whether to add to the current plot (\code{add=TRUE}) or make a new
plot (\code{add=FALSE}) (default=FALSE)}
\item{rug}{whether to add a rug plot of the event times to the current
plot (default=TRUE)}
\item{var}{specify the variable name or names for the
exposed/unexposed (names are given as characters)}
\item{\dots}{additional arguments (add to the \code{plot} command)}
}
\examples{
## The function is currently defined as
setMethod("plot", signature(x="stpm2", y="missing"),
function(x,y,newdata,type="surv",
xlab="Time",line.col=1,ci.col="grey",
add=FALSE,ci=TRUE,rug=TRUE,
var=NULL,...) {
y <- predict(x,newdata,type=type,var=var,grid=TRUE,se.fit=TRUE)
ylab <- switch(type,hr="Hazard ratio",hazard="Hazard",surv="Survival",
sdiff="Survival difference",hdiff="Hazard difference")
xx <- attr(y,"newdata")
xx <- xx[,ncol(xx)]
if (!add) matplot(xx, y, type="n", xlab=xlab, ylab=ylab, ...)
if (ci) polygon(c(xx,rev(xx)), c(y[,2],rev(y[,3])), col=ci.col, border=NA)
lines(xx,y[,1],col=line.col)
if (rug) {
Y <- x@y
eventTimes <- Y[Y[,ncol(Y)]==1,ncol(Y)-1]
rug(eventTimes)
}
})
}
\seealso{\code{\link{stpm2}}}
\keyword{methods}
%%\keyword{ ~~ other possible keyword(s)}