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dotchart2.CIs =
function (data, labels, groups = NULL, gdata = NA, horizontal = TRUE,
pch = 16, xlab = "", ylab = "", auxdata, auxgdata = NULL,
auxtitle, lty = if (.R.) 1 else 2, lines = TRUE, dotsize = 0.8,
cex = par("cex"), cex.labels = cex, cex.group.labels = cex.labels *
1.25, sort. = TRUE, add = FALSE, dotfont = par("font"),
groupfont = 2, reset.par = add, xaxis = TRUE, width.factor = 1.1,
lcolor = if (.R.) "gray" else par("col"), ...)
{
if (.R. && !add) {
plot.new()
par(new = TRUE)
}
ieaux <- if (missing(auxdata))
FALSE
else is.expression(auxdata)
mtextsrt <- function(..., srt = 0) if (.R.)
mtext(..., las = 1)
else mtext(..., srt = srt)
ndata <- length(data)
if (missing(labels)) {
if (!is.null(names(data)))
labels <- names(data)
else labels <- paste("#", seq(along = ndata))
}
else labels <- rep(as.character(labels), length = ndata)
if (missing(groups)) {
glabels <- NULL
gdata <- NULL
}
else {
if (!sort.) {
ug <- unique(as.character(groups))
groups <- factor(as.character(groups), levels = ug)
}
groups <- oldUnclass(groups)
glabels <- levels(groups)
gdata <- rep(gdata, length = length(glabels))
ord <- order(groups, seq(along = groups))
groups <- groups[ord]
data <- data[ord]
labels <- labels[ord]
if (!missing(auxdata))
auxdata <- auxdata[ord]
}
alldat <- c(data, gdata)
if (!missing(auxdata)) {
auxdata <- c(auxdata, auxgdata)
if (!ieaux)
auxdata <- format(auxdata)
}
alllab <- paste(c(labels, glabels), "")
tcex <- par("cex")
tmai <- par("mai")
oldplt <- par("plt")
if (reset.par)
on.exit(par(mai = tmai, cex = tcex, usr = tusr))
par(cex = cex)
mxlab <- 0.1 + max(strwidth(labels, units = "inches", cex = cex.labels),
if (length(glabels)) strwidth(glabels, units = "inches",
cex = cex.group.labels)) * width.factor
if (horizontal) {
tmai2 <- tmai[3:4]
if (!missing(auxdata))
tmai2[2] <- 0.2 + width.factor * max(strwidth(if (ieaux) auxdata else format(auxdata),
units = "inches", cex = cex.labels))
par(mai = c(tmai[1], mxlab, tmai2))
if (!add)
plot(alldat, seq(along = alldat), type = "n", ylab = "",
axes = FALSE, xlab = "", ...)
plot(alldat, seq(along = alldat), type = "n", ylab = "",
axes = FALSE, xlab = "", ...)
logax <- par("xaxt") == "l"
}
else {
par(mai = c(mxlab, tmai[2:4]))
if (!add)
plot(seq(along = alldat), alldat, type = "n", xlab = "",
axes = FALSE, ylab = "", ...)
logax <- par("yaxt") == "l"
}
tusr <- par("usr")
if (!add && logax) {
if (horizontal)
abline(v = 10^tusr[1:2], h = tusr[3:4])
else abline(v = tusr[1:2], h = 10^tusr[3:4])
}
else if (!add)
abline(v = tusr[1:2], h = tusr[3:4])
den <- ndata + 2 * length(glabels) + 1
if (horizontal) {
if (!add && xaxis)
mgp.axis(1, axistitle = xlab)
delt <- (-(tusr[4] - tusr[3]))/den
ypos <- seq(tusr[4], by = delt, length = ndata)
}
else {
if (!add)
mgp.axis(2, axistitle = xlab)
delt <- (tusr[2] - tusr[1])/den
ypos <- seq(tusr[1], by = delt, length = ndata)
}
if (!missing(groups)) {
ypos1 <- ypos + 2 * delt * (if (length(groups) > 1)
cumsum(c(1, diff(groups) > 0))
else 1)
diff2 <- c(3 * delt, diff(ypos1))
ypos2 <- ypos1[abs(diff2 - 3 * delt) < abs(0.001 * delt)] -
delt
ypos <- c(ypos1, ypos2) - delt
}
ypos <- ypos + delt
nongrp <- 1:ndata
if (horizontal) {
xmin <- par("usr")[1]
if (!add && lines)
abline(h = ypos[nongrp], lty = lty, lwd = 1, col = lcolor)
points(alldat, ypos, pch = pch, cex = dotsize * cex,
font = dotfont)
for (i in nongrp) { ##HAP (note, not in vertical plots yet)
N = as.numeric(auxdata[i])
CIs = binconf(alldat[i]*N, N, method="wilson")
lines(c(CIs[2], CIs[3]), c(ypos[i],ypos[i]), col="blue", lwd=1)
}
if (!add && !missing(auxdata)) {
faux <- if (ieaux)
auxdata
else paste(" ", format(auxdata), sep = "")
upedge <- par("usr")[4]
outerText(faux, ypos[nongrp], adj = 1, cex = cex.labels)
if (!missing(auxtitle)) {
auxtitle <- paste(" ", auxtitle, sep = "")
outerText(auxtitle, upedge + strheight(auxtitle,
cex = cex.labels)/2, adj = 1, cex = cex.labels,
setAside = faux[1])
}
}
if (!add) {
labng <- alllab[nongrp]
bracket <- substring(labng, 1, 1) == "[" | substring(labng,
nchar(labng), nchar(labng)) == "]"
yposng <- ypos[nongrp]
s <- !bracket
if (!is.na(any(s)) && any(s))
mtextsrt(paste(labng[s], ""), 2, 0, at = yposng[s],
srt = 0, adj = 1, cex = cex.labels)
s <- bracket
if (!is.na(any(s)) && any(s)) {
if (.R.)
text(rep(par("usr")[1], sum(s)), yposng[s],
labng[s], adj = 1, cex = cex.labels, srt = 0,
xpd = NA)
else if (.SV4. && under.unix)
text(rep(par("usr")[1], sum(s)), yposng[s],
labng[s], adj = 1, cex = cex.labels, srt = 0)
else {
xmin <- par("usr")[1] - max(nchar(labng[s])) *
0.5 * cex.labels * par("1em")[1]
text(rep(xmin, sum(s)), yposng[s], labng[s],
adj = 0, cex = cex.labels, srt = 0)
}
}
if (!missing(groups))
mtextsrt(paste(alllab[-nongrp], ""), 2, 0, at = ypos[-nongrp],
srt = 0, adj = 1, cex = cex.group.labels, font = groupfont)
}
}
else {
if (!add && lines)
abline(v = ypos[nongrp], lty = lty, lwd = 1, col = lcolor)
points(ypos, alldat, pch = pch, cex = dotsize * cex,
font = dotfont)
if (!add)
mtextsrt(alllab[nongrp], 1, 0, at = ypos[nongrp],
srt = 90, adj = 1, cex = cex.labels)
if (!add && !missing(groups))
mtextsrt(alllab[-nongrp], 1, 0, at = ypos[-nongrp],
srt = 90, adj = 1, cex = cex.group.labels, font = groupfont)
}
plt <- par("plt")
if (horizontal) {
frac <- (oldplt[2] - oldplt[1])/(oldplt[2] - plt[1])
umin <- tusr[2] - (tusr[2] - tusr[1]) * frac
tusr <- c(umin, tusr[2:4])
}
else {
frac <- (oldplt[4] - oldplt[3])/(oldplt[4] - plt[3])
umin <- tusr[4] - (tusr[4] - tusr[3]) * frac
tusr <- c(tusr[1:2], umin, tusr[4])
}
invisible()
}
plot.summary.formula.response.CIs =
function (x, which = 1, vnames = c("labels", "names"), xlim,
xlab, pch = c(16, 1, 2, 17, 15, 3, 4, 5, 0), superposeStrata = TRUE,
dotfont = 1, add = FALSE, reset.par = TRUE, main, subtitles = TRUE,
...)
{
stats <- x
stats <- oldUnclass(stats)
vnames <- match.arg(vnames)
ul <- vnames == "labels"
at <- attributes(stats)
ns <- length(at$strat.levels)
if (ns > 1 && length(which) > 1)
stop("cannot have a vector for which if > 1 strata present")
if (ns < 2)
superposeStrata <- FALSE
vn <- if (ul)
at$vlabel
else at$vname
Units <- at$vunits
vn <- ifelse(Units == "", vn, paste(vn, " [", Units, "]",
sep = ""))
vn <- vn[vn != ""]
d <- dim(stats)
n <- d[1]
nstat <- d[2]/ns
vnd <- factor(rep(vn, at$nlevels))
dn <- dimnames(stats)
if (missing(xlim))
xlim <- range(stats[, nstat * ((1:ns) - 1) + 1 + which],
na.rm = TRUE)
if (missing(main))
main <- at$funlab
nw <- length(which)
pch <- rep(pch, length = if (superposeStrata) ns else nw)
dotfont <- rep(dotfont, length = nw)
opar <- if (.R.)
par(no.readonly = TRUE)
else par()
if (reset.par)
on.exit(par(opar))
if (superposeStrata)
Ns <- apply(stats[, nstat * ((1:ns) - 1) + 1], 1, sum)
for (is in 1:ns) {
for (w in 1:nw) {
js <- nstat * (is - 1) + 1 + which[w]
z <- stats[, js]
if (missing(xlab))
xlab <- if (nw > 1)
dn[[2]][js]
else at$ylabel
dotchart2.CIs(z, groups = vnd, xlab = xlab, xlim = xlim,
auxdata = if (superposeStrata)
Ns
else stats[, js - which[w]], auxtitle = "N",
sort = FALSE, pch = pch[if (superposeStrata)
is
else w], dotfont = dotfont[w], add = add | w >
1 | (is > 1 && superposeStrata), reset.par = FALSE,
...)
lines(0.3, 0.7)
if (ns > 1 && !superposeStrata)
title(paste(paste(main, if (main != "")
" "), at$strat.levels[is]))
else if (main != "")
title(main)
if (ns == 1 && subtitles) {
title(sub = paste("N=", at$n, sep = ""), adj = 0,
cex = 0.6)
if (at$nmiss > 0)
title(sub = paste("N missing=", at$nmiss, sep = ""),
cex = 0.6, adj = 1)
}
}
}
if (superposeStrata) {
Key <- if (.R.)
function(x = NULL, y = NULL, lev, pch) {
oldpar <- par(usr = c(0, 1, 0, 1), xpd = NA)
on.exit(par(oldpar))
if (is.list(x)) {
y <- x$y
x <- x$x
}
if (!length(x))
x <- 0
if (!length(y))
y <- 1
rlegend(x, y, legend = lev, pch = pch, ...)
invisible()
}
else function(x = NULL, y = NULL, lev, pch, ...) {
if (length(x)) {
if (is.list(x)) {
y <- x$y
x <- x$x
}
key(x = x, y = y, text = list(lev), points = list(pch = pch),
transparent = TRUE, ...)
}
else key(text = list(lev), points = list(pch = pch),
transparent = TRUE, ...)
invisible()
}
formals(Key) <- list(x = NULL, y = NULL, lev = at$strat.levels,
pch = pch)
storeTemp(Key)
}
invisible()
}
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