Nothing
plot.profile.rma <- function(x, xlim, ylim, pch=19, xlab, ylab, main, refline=TRUE, cline=FALSE, ...) {
#########################################################################
mstyle <- .get.mstyle("crayon" %in% .packages())
.chkclass(class(x), must="profile.rma")
.start.plot()
if (dev.cur() == 1) {
par(mfrow=n2mfrow(x$comps))
#on.exit(par(mfrow=c(1,1)), add=TRUE)
}
missing.xlim <- missing(xlim)
missing.ylim <- missing(ylim)
missing.xlab <- missing(xlab)
missing.ylab <- missing(ylab)
missing.main <- missing(main)
### filter out some arguments for the plot() function
lplot <- function(..., time, LB, startmethod, sub1) plot(...)
lpoints <- function(..., time, LB, startmethod, sub1, log) points(...) # need 'log' here so profile(res, log="x") doesn't throw a warning
#########################################################################
if (x$comps == 1) {
if (missing.xlim)
xlim <- x$xlim
if (missing.ylim)
ylim <- x$ylim
if (missing.xlab)
xlab <- x$xlab
if (missing.ylab)
ylab <- paste(ifelse(x$method=="REML", "Restricted ", ""), "Log-Likelihood", sep="")
if (missing.main)
main <- x$title
if (min(x[[1]]) <= x$vc && max(x[[1]]) >= x$vc) {
pos <- which(x[[1]] >= x$vc)[1]
x[[1]] <- c(x[[1]][seq_len(pos-1)], x$vc, x[[1]][pos:length(x[[1]])])
x[[2]] <- c(x[[2]][seq_len(pos-1)], x$maxll, x[[2]][pos:length(x[[2]])])
}
lplot(x[[1]], x[[2]], type="n", xlab=xlab, ylab=ylab, main=main, bty="l", xlim=xlim, ylim=ylim, ...)
if (refline) {
abline(v=x$vc, lty="dotted")
abline(h=x$maxll, lty="dotted")
}
if (cline)
abline(h=x$maxll - qchisq(0.95, df=1)/2, lty="dotted")
lpoints(x[[1]], x[[2]], type="o", pch=pch, ...)
} else {
for (j in seq_len(x$comps)) {
if (missing.xlim)
xlim <- x[[j]]$xlim
if (missing.ylim)
ylim <- x[[j]]$ylim
if (missing.xlab) {
xlab <- x[[j]]$xlab
} else {
if (length(xlab) == 1L) {
xlab <- rep(xlab, x$comps)
}
}
if (missing.ylab) {
ylab <- paste(ifelse(x[[j]]$method=="REML", "Restricted ", ""), "Log-Likelihood", sep="")
} else {
if (length(ylab) == 1L) {
ylab <- rep(ylab, x$comps)
}
}
if (missing.main) {
main <- x[[j]]$title
} else {
if (length(main) == 1L) {
main <- rep(main, x$comps)
}
}
lplot(x[[j]], xlim=xlim, ylim=ylim, pch=pch,
xlab=if (missing.xlab) xlab else xlab[j],
ylab=if (missing.ylab) ylab else ylab[j],
main=if (missing.main) main else main[j],
cline=cline, ...)
}
}
}
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