#' dotplot.errors
#'
#' build a vertical dotplot with error bars
#'
#' @param x dataframe
#' @param myTheme default values for pch and col (todo)
#' @param qlabel text for axis label
#' @param add.text.to.qlabel additional text for axis label
#' @param type.bar default is "CI"
#' @param conf.level default is .95
#' @param end.length default is .05
#' @param reorder.groups default is TRUE
#' @param reordering order of sorting when reorder.groups is TRUE
#' @param label.define (todo)
#' @param reference.line value for the reference line. default is null
#' @param bar.color default is 1
#' @param horizontal layout of the dotplot. default is TRUE
#' @param ... further arguments passed to or from other methods.
#' @author Rollie Parrish
#' @export
dotplot.errors <- function (x, myTheme = simpleTheme(pch = 19, col = 1), qlabel = "Estimated rate",
add.text.to.qlabel = "", type.bar = "CI", conf.level = 0.95,
end.length = 0.05, reorder.groups = TRUE, reordering = "decreasing",
label.define = list(), reference.line = NULL, bar.color = 1,
horizontal = TRUE, ...)
{
o <- c(which(colnames(x) == "group"), which(colnames(x) ==
"lower"), which(colnames(x) == "est"), which(colnames(x) ==
"upper"))
if (length(o) != 4)
stop("Error: Incorrect data frame")
x <- x[, o]
x$group <- factor(x$group)
if (horizontal == T)
hor <- 1
else hor <- -1
if (reordering == "decreasing")
FUN.to.reorder <- function(x) mean(x) * hor
else FUN.to.reorder <- function(x) -mean(x) * hor
if (reorder.groups)
x$group <- with(x, reorder(group, est, FUN = FUN.to.reorder))
if (reorder.groups) {
if (reordering == "increasing") {
x$group = factor(x$group, levels = x$group[order(-x$est,
-x$lower, -x$upper, -x$group)], ordered = TRUE)
}
else {
x$group = factor(x$group, levels = x$group[order(x$est,
x$lower, x$upper, x$group)], ordered = TRUE)
}
}
if (type.bar == "CI")
xlab <- substitute(lab %+-% CL, list(lab = qlabel, CL = paste(" ",
as.character(conf.level * 100), "% CI", add.text.to.qlabel,
sep = "")))
else if (type.bar == "SE")
xlab <- substitute(lab %+-% " SE" ~ ~AT, list(lab = qlabel,
AT = add.text.to.qlabel))
else xlab <- substitute(lab %+-% Type.bar ~ ~AT, list(lab = qlabel,
Type.bar = type.bar, AT = add.text.to.qlabel))
if (horizontal == T)
p <- stripplot(group ~ est, data = x, lower = x$lower,
upper = x$upper, xlim = range(x[, 2:4]) + c(-0.04,
0.04) * diff(range(x[, 2:4])), xlab = c(list(xlab),
label.define), par.settings = myTheme, panel = function(x,
y, lower, upper, ..., subscripts) {
if (is.null(reference.line) == F)
panel.abline(v = reference.line, col = "grey")
panel.abline(h = y, col = "grey", lty = "dashed")
panel.arrows(x0 = lower[subscripts], y0 = y,
x1 = upper[subscripts], y1 = y, angle = 90,
code = 3, length = end.length, col = bar.color)
panel.stripplot(x, y, ...)
}, ...)
else p <- stripplot(est ~ group, data = x, lower = x$lower,
upper = x$upper, ylim = range(x[, 2:4]) + c(-0.04, 0.04) *
diff(range(x[, 2:4])), ylab = c(list(xlab), label.define),
par.settings = myTheme, panel = function(x, y, lower,
upper, ..., subscripts) {
if (is.null(reference.line) == F)
panel.abline(h = reference.line, col = "grey")
panel.abline(v = x, col = "grey", lty = "dashed")
panel.arrows(y0 = lower[subscripts], x0 = x, y1 = upper[subscripts],
x1 = x, angle = 90, code = 3, length = end.length,
col = bar.color)
panel.stripplot(x, y, ...)
}, ...)
return(p)
}
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