R: Hazard Ratio Plot

hazard.ratio.plot {Design}

R Documentation

Hazard Ratio Plot

Description

The hazard.ratio.plot function repeatedly estimates Cox regression coefficients and confidence limits within time intervals. The log hazard ratios are plotted against the mean failure/censoring time within the interval. Unless times is specified, the number of time intervals will be max(round(d/e),2), where d is the total number of events in the sample. Efron's likelihood is used for estimating Cox regression coefficients (using coxph.fit). In the case of tied failure times, some intervals may have a point in common.

Usage

hazard.ratio.plot(x, Srv, which, times=, e=30, subset,
                  conf.int=.95, legendloc=NULL, smooth=TRUE, pr=FALSE, pl=TRUE,
                  add=FALSE, ylim, cex=.5, xlab="t", ylab, antilog=FALSE, ...)

Arguments

`x`	a vector or matrix of predictors
`Srv`	a Surv object
`which`	a vector of column numbers of `x` for which to estimate hazard ratios across time and make plots. The default is to do so for all predictors. Whenever one predictor is displayed, all other predictors in the `x` matrix are adjusted for (with a separate adjustment form for each time interval).
`times`	optional vector of time interval endpoints. Example: `times=c(1,2,3)` uses intervals `[0,1), [1,2), [2,3), [3+)`. If times is omitted, uses intervals containing `e` events
`e`	number of events per time interval if times not given
`subset`	vector used for subsetting the entire analysis, e.g. `subset=sex=="female"`
`conf.int`	confidence interval coverage
`legendloc`	location for legend. Omit to use mouse, `"none"` for none, `"ll"` for lower left of graph, or actual x and y coordinates (e.g. `c(2,3)`)
`smooth`	also plot the super–smoothed version of the log hazard ratios
`pr`	defaults to `FALSE` to suppress printing of individual Cox fits
`pl`	defaults to `TRUE` to plot results
`add`	add this plot to an already existing plot
`ylim`	vector of `y`-axis limits. Default is computed to include confidence bands.
`cex`	character size for legend information, default is 0.5
`xlab`	label for `x`-axis, default is `"t"`
`ylab`	label for `y`-axis, default is `"Log Hazard Ratio"` or `"Hazard Ratio"`, depending on `antilog`.
`antilog`	default is `FALSE`. Set to `TRUE` to plot anti-log, i.e., hazard ratio.
`...`	optional graphical parameters

Author(s)

Frank Harrell
Department of Biostatistics, Vanderbilt University
f.harrell@vanderbilt.edu

Examples

n <- 500
set.seed(1)
age <- 50 + 12*rnorm(n)
cens <- 15*runif(n)
h <- .02*exp(.04*(age-50))
d.time <- -log(runif(n))/h
label(d.time) <- 'Follow-up Time'
e <- ifelse(d.time <= cens,1,0)
d.time <- pmin(d.time, cens)
units(d.time) <- "Year"
hazard.ratio.plot(age, Surv(d.time,e), e=20, legendloc='ll')