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pairs.profileModel <- function(x, colours = 2:3, title = NULL, ...) {
## 'pairs.profileModel' is a minor modification of 'pairs.profile' in the
# MASS lirary.
#'pairs.profile' was modified by Ioannis Kosmidis under GPL 2 or greater
# and after the permission of the authors, in order to comply with objects
# of class "profileModel".
# Ioannis Kosmidis <I.Kosmidis@warwick.ac.uk> [15/02/2008]
#
## Another plot method for profile objects showing pairwise traces.
# Recommended only for diagnostic purposes
######### Begin
## Addition by Ioannis Kosmidis [15/02/2008]
if (!attr(x, "includes.traces")) {
cat("Updating to get profile traces...\n")
x <- update(x, verbose = FALSE, profTraces = TRUE)
}
######### End
######### Begin
## Modification by Ioannis Kosmidis [15/02/2008]
isnotNA <- !x$isNA
profNames <- names(x$profiles[isnotNA])
parvals <- lapply(x$profiles[isnotNA], FUN = function(obj) obj[, -2])
parvals <- lapply(parvals, FUN = function(obj) obj[, profNames])
rng <- apply(do.call("rbind", parvals), 2, range, na.rm = TRUE)
Pnames <- colnames(rng)
npar <- length(Pnames)
coefs <- coef(x$fit)[isnotNA]
form <- paste(as.character(formula(x$fit))[c(2, 1, 3)], collapse = "")
######### End
oldpar <- par(mar = c(0, 0, 0, 0), mfrow = c(1, 1), oma = c(3,
3, 6, 3), las = 1)
on.exit(par(oldpar))
##
## The following dodge ensures that the plot region is square
##
fin <- par("fin")
dif <- (fin[2] - fin[1])/2
if (dif > 0)
adj <- c(dif, 0, dif, 0)
else adj <- c(0, -dif, 0, -dif)
par(omi = par("omi") + adj)
##
##
cex <- 1 + 1/npar
frame()
mtext(form, side = 3, line = 3, cex = 1.5, outer = TRUE)
del <- 1/npar
for (i in 1:npar) {
ci <- npar - i
pi <- Pnames[i]
for (j in 1:npar) {
pj <- Pnames[j]
par(fig = del * c(j - 1, j, ci, ci + 1))
if (i == j) {
par(new = TRUE)
plot(rng[, pj], rng[, pi], axes = FALSE, xlab = "",
ylab = "", type = "n")
op <- par(usr = c(-1, 1, -1, 1))
text(0, 0, pi, cex = cex, adj = 0.5)
par(op)
}
else {
col <- colours
if (i < j)
col <- col[2:1]
if (!is.null(parvals[[pj]])) {
par(new = TRUE)
plot(spline(x <- parvals[[pj]][, pj], y <- parvals[[pj]][,
pi]), type = "l", xlim = rng[, pj], ylim = rng[,
pi], axes = FALSE, xlab = "", ylab = "",
col = col[2])
pu <- par("usr")
smidge <- 2/100 * (pu[4] - pu[3])
segments(x, pmax(pu[3], y - smidge), x, pmin(pu[4],
y + smidge))
}
else plot(rng[, pj], rng[, pi], axes = FALSE,
xlab = "", ylab = "", type = "n")
if (!is.null(parvals[[pi]])) {
lines(x <- parvals[[pi]][, pj], y <- parvals[[pi]][,
pi], type = "l", col = col[1])
pu <- par("usr")
smidge <- 2/100 * (pu[2] - pu[1])
segments(pmax(pu[1], x - smidge), y, pmin(pu[2],
x + smidge), y)
}
points(coefs[pj], coefs[pi], pch = 3, cex = 3)
}
if (i == npar)
axis(1)
if (j == 1)
axis(2)
if (i == 1)
axis(3)
if (j == npar)
axis(4)
}
}
par(fig = c(0, 1, 0, 1))
if (!is.null(title)) {
par(oma = c(0, 0, 2, 0))
title(title, outer = TRUE)
}
invisible(x)
}
plot.profileModel <- function(x, cis = NULL, signed = FALSE, interpolate = TRUE,
n.interpolations = 100, print.grid.points = FALSE, title = NULL,
...) {
fitted <- x$fit
if (!is.null(cis)) {
fitted.name <- x$call[["fitted"]]
prof.name <- match.call()[["x"]]
fitted.attr <- attr(cis, "fitted object")
prof.attr <- attr(cis, "profileModel object")
if (is.null(fitted.attr))
fitted.attr <- 1
if (is.null(prof.attr))
prof.attr <- 1
if (fitted.name == fitted.attr | prof.name == prof.attr) {
}
else stop("Invalid confidence intervals were supplied.")
}
if (!(agreement <- x$agreement) & signed)
stop("The objective and the fitting procedure ", fitted$call[[1]],
" do not agree. Signed square roots cannot be calculated.")
op <- par(no.readonly = TRUE)
if (is.null(x$quantile)) {
if (signed) {
x <- signedSquareRoots.profileModel(x)
temp.plot <- function(mat, nam) {
plot(mat[, 1], mat[, 2], type = "l", xlab = nam,
ylab = "Signed sqrt of objective")
}
}
else {
temp.plot <- function(mat, nam) {
plot(mat[, 1], mat[, 2], type = "l", xlab = nam,
ylab = "Profiled objective")
}
}
}
else {
if (signed) {
x <- signedSquareRoots.profileModel(x)
temp.plot <- function(mat, nam) {
plot(mat[, 1], mat[, 2], type = "l", xlab = nam,
ylab = "Signed sqrt of objective")
points(x = c(min(mat[, 1]), max(mat[, 1])), y = rep(-sqrt(x$quantile),
2), type = "l", lty = 2)
points(x = c(min(mat[, 1]), max(mat[, 1])), y = rep(sqrt(x$quantile),
2), type = "l", lty = 2)
}
}
else temp.plot <- function(mat, nam) {
plot(mat[, 1], mat[, 2], type = "l", xlab = nam,
ylab = "Profiled objective")
points(x = c(min(mat[, 1]), max(mat[, 1])), y = rep(x$quantile,
2), type = "l", lty = 2)
}
}
profRes.or <- profRes <- x$profiles
isNA <- x$isNA
p <- length(profRes)
profNames <- names(profRes)
which <- x$profiled.parameters
scale <- !is.null(Xmax <- fitted$X.max.scaleFit)
Betas <- coef(fitted)[which]/(if (scale)
Xmax[which]
else 1)
if (agreement) {
res.at.betas <- as.list(rep(NA, p))
names(res.at.betas) <- profNames
for (i in 1:p) {
if (isNA[i])
next
res.at.betas[[profNames[i]]] <- matrix(c(Betas[i],
0), 1, 2)
}
}
else suppressWarnings(res.at.betas <- update(x, grid.bounds = cbind(Betas,
Betas), gridsize = 1, quantile = NULL, verbose = FALSE,
profTraces = FALSE)$profiles)
if (interpolate) {
for (i in 1:p) {
if (isNA[i])
next
profRes.i <- profRes[[i]][, 1:2]
### construct some information for the spline to use
lin <- approx(profRes.i, n = 2 * nrow(profRes.i))
smoothed <- spline(lin, n = n.interpolations)
profRes[[i]] <- cbind(smoothed$x, smoothed$y)
}
}
intersects <- x$intersects
has.prelim <- attr(x$grid.bounds, "from.prelim")
par(mfrow = c(ceiling(sqrt(p)), ceiling(sqrt(p))))
for (i in 1:p) {
if (isNA[i])
next
profRes.i <- profRes[[i]]
profNames.i <- profNames[i]
temp.plot(profRes.i, profNames.i)
min.i <- min(profRes.i[, 2])
max.i <- max(profRes.i[, 2])
if (has.prelim) {
intersects.i <- intersects[i, ]
# draw cis
if (!is.null(cis)) {
cis.i <- cis[i, ]
if (all(intersects.i)) {
points(x = rep(cis.i[1], 2), y = c(min.i, max.i),
type = "l", lty = 3)
points(x = cis.i[1], y = min.i, pch = 6)
points(x = rep(cis.i[2], 2), y = c(min.i, max.i),
type = "l", lty = 3)
points(x = cis.i[2], y = min.i, pch = 6)
}
if (sum(intersects.i) == 1) {
which.intersects.i <- which(intersects.i)
points(x = rep(cis.i[which.intersects.i], 2),
y = c(min.i, max.i), type = "l", lty = 3)
points(x = cis.i[which.intersects.i], y = min.i,
pch = 6)
}
}
# draw estimates
if (all(intersects.i) | all(!intersects.i)) {
points(res.at.betas[[i]], pch = 4)
}
else {
which.intersects.i <- which(intersects.i)
if (which.intersects.i == 1) {
if (agreement)
text(x = max(profRes.i[, 1]), y = 0, labels = expression(infinity))
else text(x = max(profRes.i[, 1]), y = min.i,
labels = expression(infinity))
}
if (which.intersects.i == 2) {
if (agreement)
text(x = min(profRes.i[, 1]), y = 0, labels = expression(-infinity))
else text(x = min(profRes.i[, 1]), y = min.i,
labels = expression(-infinity))
}
if (!agreement)
points(res.at.betas[[i]], pch = 4)
}
}
if (print.grid.points)
points(x = profRes.or[[i]][, 1], y = profRes.or[[i]][,
2], pch = 16, cex = 0.6)
title(profNames.i)
}
######### Begin
## Addition by Ioannis Kosmidis [15/02/2008]
if (!is.null(title)) {
par(oma = c(0, 0, 2, 0))
title(title, outer = TRUE)
}
######### End
par(op)
}
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