#completely taken from dotchart with some minor addition of confidence intervals
#July 17, 2016
#input is the mean + standard errors, and (optionally, alpha)
"error.dots" <-
function (x,var=NULL, se=NULL, head = 12, tail = 12, sort=TRUE,decreasing=FALSE,alpha=.05,eyes=FALSE, min.n = NULL,max.labels =40, labels = NULL, groups = NULL, gdata = NULL, cex = par("cex"),
pt.cex = cex, pch = 21, gpch = 21, bg = par("bg"), color = par("fg"),
gcolor = par("fg"), lcolor = "gray", xlim = range(x[is.finite(x)]),
main = NULL, xlab = NULL, ylab = NULL, ...)
{
opar <- par("mai", "mar", "cex", "yaxs")
on.exit(par(opar))
par(cex = cex, yaxs = "i")
#first, see if the data come from a psych object with sd and n or se
if(length(class(x)) > 1 ) {if (class(x)[1] == "psych") {obj <- class(x)[2]
switch(obj,
statsBy = {if(is.null(min.n)) {se <- x$sd[,var]/sqrt(x$n[,var])
x <- x$mean[,var] } else {se <- x$sd[,var]
n.obs <- x$n[,var]
x <- x$mean[,var]
x <- subset(x,n.obs > min.n)
se <- subset(se,n.obs > min.n)
n.obs <- subset(n.obs, n.obs > min.n)
se <- se/sqrt(n.obs)
}},
describe = {se <- x$se
labels <- rownames(x)
x <- x$mean
names(x) <- labels
}
)
} #end switch
n.var <- length(x)
if(!is.null(se)) {ci <- qnorm((1-alpha/2))*se} else {ci <- NULL}
if (sort) { ord <- order(x,decreasing=decreasing) } else {ord <- n.var:1}
x <- x[ord]
se <- se[ord]
temp <- temp.se <- rep(NA,min(head+tail,n.var))
if((head+tail) < n.var) {
if (head > 0 ){ temp[1:head] <- x[1:head]
temp.se[1:head] <- se[1:head]
names(temp) <- names(x)[1:head]
}
if(tail > 0 ) {temp[(head + 1):(head + tail)] <- x[(length(x)-tail+1):length(x)]
temp.se[(head + 1):(head + tail)] <- se[(length(x)-tail+1):length(x)]
names(temp)[(head + 1):(head + tail)] <- names(x)[(length(x)-tail+1):length(x)]
}
x <- temp
se <- temp.se
}
labels <- names(x)
if(!is.null(se)) {ci <- qnorm((1-alpha/2))*se} else {ci <- NULL}
if(!is.null(ci)) xlim <- c(min(x - ci),max(x + ci))
labels <- substr(labels,1,max.labels)
if(eyes) { #get ready to draw catseyes
ln <- seq(-3,3,.1)
rev <- (length(ln):1)
}
if (!is.numeric(x))
stop("'x' must be a numeric vector or matrix")
n <- length(x)
if (is.matrix(x)) {
if (is.null(labels))
labels <- rownames(x)
if (is.null(labels))
labels <- as.character(1L:nrow(x))
labels <- rep_len(labels, n)
if (is.null(groups))
groups <- col(x, as.factor = TRUE)
glabels <- levels(groups)
}
else {
if (is.null(labels))
labels <- names(x)
glabels <- if (!is.null(groups))
levels(groups)
if (!is.vector(x)) {
warning("'x' is neither a vector nor a matrix: using as.numeric(x)")
x <- as.numeric(x)
}
}
plot.new()
linch <- if (!is.null(labels))
max(strwidth(labels, "inch"), na.rm = TRUE)
else 0
if (is.null(glabels)) {
ginch <- 0
goffset <- 0
}
else {
ginch <- max(strwidth(glabels, "inch"), na.rm = TRUE)
goffset <- 0.4
}
if (!(is.null(labels) && is.null(glabels))) {
nmai <- par("mai")
nmai[2L] <- nmai[4L] + max(linch + goffset, ginch) +
0.1
par(mai = nmai)
}
if (is.null(groups)) {
o <- 1L:n
y <- o
ylim <- c(0, n + 1)
}
else {
o <- sort.list(as.numeric(groups), decreasing = TRUE)
x <- x[o]
groups <- groups[o]
color <- rep_len(color, length(groups))[o]
lcolor <- rep_len(lcolor, length(groups))[o]
offset <- cumsum(c(0, diff(as.numeric(groups)) != 0))
y <- 1L:n + 2 * offset
ylim <- range(0, y + 2)
}
plot.window(xlim = xlim, ylim = ylim, log = "")
lheight <- par("csi")
if (!is.null(labels)) {
linch <- max(strwidth(labels, "inch"), na.rm = TRUE)
loffset <- (linch + 0.1)/lheight
labs <- labels[o]
mtext(labs, side = 2, line = loffset, at = y, adj = 0,
col = color, las = 2, cex = cex, ...)
}
abline(h = y, lty = "dotted", col = lcolor)
points(x, y, pch = pch, col = color, bg = bg, cex = pt.cex/cex)
if(!is.null(ci)) {if(!eyes) {
segments(x - ci, y, x+ci, y,
col = par("fg"), lty = par("lty"), lwd = par("lwd"))
} else {catseyes(x,y,se=se,n=NULL,alpha=alpha,density=-10)}}
if (!is.null(groups)) {
gpos <- rev(cumsum(rev(tapply(groups, groups, length)) +
2) - 1)
ginch <- max(strwidth(glabels, "inch"), na.rm = TRUE)
goffset <- (max(linch + 0.2, ginch, na.rm = TRUE) + 0.1)/lheight
mtext(glabels, side = 2, line = goffset, at = gpos, adj = 0,
col = gcolor, las = 2, cex = cex, ...)
if (!is.null(gdata)) {
abline(h = gpos, lty = "dotted")
points(gdata, gpos, pch = gpch, col = gcolor, bg = bg,
cex = pt.cex/cex, ...)
}
}
axis(1)
box()
title(main = main, xlab = xlab, ylab = ylab, ...)
invisible()
}
}
#not used here --
"catseyes" <- function(x,y,ci,density=density,col=col) {
SCALE=.7
ln <- seq(-3,3,.1)
rev <- (length(ln):1)
norm <- dnorm(ln)
clim <- qnorm(alpha/2)
norm <- dt(ln,n-1)
clim <- qt(alpha/2,n-1)
norm <- c(norm,-norm[rev])
ln <- seq(-3,3,.1)
cln <- seq(clim,-clim,.01)
cnorm <- dnorm(cln)
cnorm <- c(0,cnorm,0,-cnorm,0) #this closes the probability interval
polygon(norm*SCALE+x,c(ln,ln[rev])*se+y)
polygon(cnorm*SCALE+x,c(clim,cln,-clim,-cln,clim)*se+y,density=density,col=col)}
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