Dear all,
I've modified the plot.cox.zph function to allow
customized xlab and ylab (see below). Someone might
like to confirm that it works.
Thanks for all the assistance.
Dan
___________________________________
plot.cox.zph <- function (x, resid = TRUE, se = TRUE,
df = 4, nsmo = 40, var,
xlab="Time",ylab = paste("Beta(t) for",
dimnames(yy)[[2]]),...)
{
xx <- x$x
yy <- x$y
d <- nrow(yy)
df <- max(df)
nvar <- ncol(yy)
pred.x <- seq(from = min(xx), to = max(xx), length
= nsmo)
temp <- c(pred.x, xx)
lmat <- ns(temp, df = df, intercept = TRUE)
pmat <- lmat[1:nsmo, ]
xmat <- lmat[-(1:nsmo), ]
qmat <- qr(xmat)
if (se) {
bk <- backsolve(qmat$qr[1:df, 1:df], diag(df))
xtx <- bk %*% t(bk)
seval <- d * ((pmat %*% xtx) * pmat) %*%
rep(1, df)
}
if (missing(var))
var <- 1:nvar
else {
if (is.character(var))
var <- match(var, dimnames(yy)[[2]])
if (any(is.na(var)) || max(var) > nvar ||
min(var) <
1)
stop("Invalid variable requested")
}
if (x$transform == "log") {
xx <- exp(xx)
pred.x <- exp(pred.x)
}
else if (x$transform != "identity") {
xtime <- as.numeric(dimnames(yy)[[1]])
apr1 <- approx(xx, xtime, seq(min(xx),
max(xx), length = 17)[2 *
(1:8)])
temp <- signif(apr1$y, 2)
apr2 <- approx(xtime, xx, temp)
xaxisval <- apr2$y
xaxislab <- rep("", 8)
for (i in 1:8) xaxislab[i] <- format(temp[i])
}
for (i in var) {
y <- yy[, i]
yhat <- pmat %*% qr.coef(qmat, y)
if (resid)
yr <- range(yhat, y)
else yr <- range(yhat)
if (se) {
temp <- 2 * sqrt(x$var[i, i] * seval)
yup <- yhat + temp
ylow <- yhat - temp
yr <- range(yr, yup, ylow)
}
if (x$transform == "identity")
plot(range(xx), yr, type = "n", xlab =
xlab, ylab = ylab[i],
...)
else if (x$transform == "log")
plot(range(xx), yr, type = "n", xlab =
xlab, ylab = ylab[i],
log = "x", ...)
else {
plot(range(xx), yr, type = "n", xlab =
xlab, ylab = ylab[i],
axes = FALSE, ...)
axis(1, xaxisval, xaxislab)
axis(2)
box()
}
if (resid)
points(xx, y)
lines(pred.x, yhat)
if (se) {
lines(pred.x, yup, lty = 2)
lines(pred.x, ylow, lty = 2)
}
}
}
--- Thomas Lumley <[EMAIL PROTECTED]> wrote:
> On Mon, 11 Jul 2005, Adaikalavan Ramasamy wrote:
>
> > I am not sure if there is an easy way around this.
> An ugly hack is to
> > make a copy the function "survival:::plot.cox.zph"
> and make your
> > modified function. But there are others in the
> list who might know
> > neater solutions.
>
> If you then send a patch to the package maintainer
> it stops being an ugly
> hack and turns into an example of collaborative
> open-source development :)
>
> -thomas
>
>
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