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#' @rdname CIplot
#' @include CIplot.R
#'
#' @method CIplot default
#' @export
#'
#' @param x \code{default}: \code{matrix} or \code{data.frame} class
#' with 3 columns ('any name', \code{lwr}, \code{upr}),
#' or an object: \code{htest}, \code{TukeyHSD},
#' \code{glht} (\pkg{multcomp}),
#' \code{glm} (logistic regression only!)
#' or \code{posthocTGH} (\pkg{userfriendlyscience}).
#' @param xlog (logical) if \code{log} is \code{TRUE},
#' the x axis is drawn logarithmically.
#' Default is \code{FALSE}.
#' @param xlab a title for the plot.
#' @param xlim the x limits (x1, x2) of the plot.
#' @param yname If \code{yname} is \code{TRUE},
#' the name of comparison between groups are shown.
#' @param las numeric in {0,1,2,3}; the style of axis labels.
#' Default is 0. see also \code{par}.
#' @param pch plotting 'character', i.e., symbol to use.
#' @param pcol color code or name of the points.
#' @param pcolbg background (fill) color for the open plot symbols
#' given by 'pch = 21:25'.
#' @param pcex character (or symbol) expansion of points.
#' @param conf.level \code{default} and \code{glm} object only.
#' the confidence interval. Default is 0.95.
#' see also \code{\link{ORci}}.
#' @param cilty line types of conficence intervals.
#' @param cilwd line width of conficence intervals.
#' @param cicol color code or name of conficence intervals.
#' @param v the x-value(s) for vertical line.
#' @param vlty line types of vertical line.
#' @param vlwd line width of vertical line.
#' @param vcol color code or name of vertical line.
#' @param main a main title for the plot.
#' @param \dots other options for x-axis.
#'
#' @examples
#' ##### default (matrix or data.frame)
#' require(graphics)
#' x <- matrix(c(3, 1, 5,
#' 4, 2, 6), 2, 3, byrow = TRUE)
#' colnames(x) <- c("esti", "lwr", "upr")
#' rownames(x) <- c("A", "B")
#' CIplot(x, xlab = "difference", v = 2, las = 1)
#'
#' @keywords plot
#'
## x: matrix or data.frame(estimation, lwr, upr)
## v: required
CIplot.default <-
function(x,
xlog = FALSE, xlim = NULL, xlab = NULL, ## x-axis
yname = TRUE, las = 0, ## y-axis
pch = 21, pcol = 1, pcolbg = "white", pcex = 1, ## points
conf.level = 0.95, cilty = 1, cilwd = 1, cicol = 1, ## conf.int
v, vlty = 2, vlwd = 1, vcol = 1, ## vertical
main = NULL, ## Title
...)
{
if (ncol(x) < 3L) {
stop("x is required at least 3 columns.\n")
}
if (is.matrix(x)) x <- as.data.frame(x)
if (is.null(main)) {
main <- paste0(format(100 * conf.level, digits = 2L),
"% confidence interval")
}
xi <- x[,1:3] ## estimation, lwr, upr
yvals <- nrow(xi):1L
if (is.null(xlim)) xlim <- c(min(xi), max(xi))
plot(c(xi[,"lwr"], xi[,"upr"]), rep.int(yvals, 2L),
type = "n", axes = FALSE,
xlab = xlab, ylab = "",
xlim = xlim, log = ifelse(xlog, "x", ""),
ylim = c(0.5, nrow(xi) + 0.5),
main = main)
axis(1, ...)
if (yname) {
axis(2, at = nrow(xi):1,
labels = dimnames(xi)[[1L]], las = las)
}
abline(v = v, lty = vlty, lwd = vlwd, col = vcol)
arrows(xi[, "lwr"], yvals, xi[, "upr"], yvals,
code = 3, angle = 90, length = 0.15,
lty = cilty, lwd = cilwd, col = cicol)
points(xi[, 1], yvals, pch = pch, cex = pcex,
col = pcol, bg = pcolbg)
box()
}
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