#SCCS @(#)plot.cox.zph.s	4.6 08/13/96
plot.cox.zph <- function(x, resid=TRUE, se=TRUE, df=4, nsmo=40, var, ...) {
    ##require(splines)
    xx <- x$x
    yy <- x$y
    d <- nrow(yy)
    df <- max(df)     #error proofing
    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,]       # for prediction
    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)
	}

    ylab <- paste("Beta(t) for", dimnames(yy)[[2]])
    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")
	}

    #
    # Figure out a 'good' set of x-axis labels.  Find 8 equally spaced
    #    values on the 'transformed' axis.  Then adjust until they correspond
    #    to rounded 'true time' values.  Avoid the edges of the x axis, or
    #    approx() may give a missing value
    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$transform=='identity')
	    plot(range(xx), yr, type='n', xlab="Time", ylab=ylab[i], ...)
	else if (x$transform=='log')
	    plot(range(xx), yr, type='n', xlab="Time", ylab=ylab[i], log='x',
			...)
	else {
	    plot(range(xx), yr, type='n', xlab="Time", 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)
	    }
	}
    }
