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#' Print result held in \code{htest_boot} object
#'
#' \code{print.htest_boot} prints a return value held in a list of
#' class \code{'htest_boot'}, as returned by e.g.,
#' \code{\link{nestedRanksTest}}. Class \code{'htest_boot'}
#' extends class \code{'htest'} by including group weights, the
#' number of bootstrap iterations, and the complete null distribution.
#' The latter is not printed by this function; it may be visualised with
#' \code{\link{plot.htest_boot}}.
#'
#' @param x Value of class \code{'htest_boot'} as returned by
#' e.g., \code{nestedRanksTest}.
#'
#' @param digits Number of digits or significant digits to use in output.
#' Similar to other \code{print} methods, this method pays attention to
#' the \code{"digits"} option.
#'
#' @param prefix String, passed to \code{\link{print.htest}}
#'
#' @param \dots Additional arguments passed to \code{print.htest}.
#'
#' @return The value of x is returned invisibly.
#'
#' @examples
#' data(woodpecker_multiyear)
#' ## n.iter set to 1000 to shorten completion time
#' res <- nestedRanksTest(Distance ~ Year | Granary, n.iter = 1000,
#' data = woodpecker_multiyear,
#' subset = Species == "agrifolia")
#' class(res)
#' print(res)
#'
#' @seealso \code{\link{plot.htest_boot}} for a graphical plot of test
#' results, \code{\link{print.htest}} for the print method of
#' the base class, and \code{\link{nestedRanksTest}} for one test that
#' returns an object of class \code{'htest_boot'}
#'
#' @export
#'
print.htest_boot <- function(x, digits = getOption("digits"), prefix = "\t", ...)
{
NextMethod(x, digits = digits, prefix = prefix, ...)
cat("bootstrap iterations:", x$n.iter, "\ngroup weights:\n")
print(x$weights, digits = digits, ...)
invisible(x)
}
#' Diagnostic plot of result held in \code{htest_boot} object
#'
#' \code{plot.htest_boot} creates a diagnostic plot of a return value
#' held in a list of class \code{'htest_boot'}, as returned by e.g.,
#' \code{\link{nestedRanksTest}}. The plot contains a histogram of the
#' null distribution generated by' bootstrapping plotted with
#' \code{\link{hist}}, and a verticle line indicating the observed value
#' plotted with \code{\link{abline}}.
#'
#' If there is no null distribution included in the class, e.g., because
#' the' options \code{lightweight = TRUE} or \code{n.iter = 1} were given to
#' \code{nestedRanksTest}, this function produces an error.
#'
#' @param x Value of class \code{'htest_boot'}
#' @param breaks The number of breaks to use when plotting the distribution,
#' the default is calculated from \code{n.iter} of the call to
#' \code{nestedRanksTest}
#' @param col Fill color for histogram bars, passed to \code{hist}.
#' @param border Border color for histogram bars, passed to \code{hist}
#' @param digits Number of digits to use for statistic and p-value, the
#' default is taken from the \code{"digits"} option
#' @param main Main title, passed to \code{hist}
#' @param xlab X-axis label, passed to \code{hist}
#' @param ylab Y-axis label, passed to \code{hist}
#' @param p.col Observed value line colour, passed to \code{abline}
#' @param p.lty Observed value line type, passed to \code{abline}
#' @param p.lwd Observed value line width, passed to \code{abline}
#' @param \dots Additional arguments passed to \code{hist} and
#' \code{abline} for plotting
#'
#' @return None
#'
#' @examples
#' require(graphics)
#'
#' data(woodpecker_multiyear)
#'
#' ## n.iter set to 1000 to shorten completion time
#' res.a <- nestedRanksTest(Distance ~ Year | Granary, n.iter = 1000,
#' data = woodpecker_multiyear,
#' subset = Species == "agrifolia")
#' res.l <- nestedRanksTest(Distance ~ Year | Granary, n.iter = 1000,
#' data = woodpecker_multiyear,
#' subset = Species == "lobata")
#'
#' opa = par(mfrow = c(2, 1))
#' ## Defaults
#' plot(res.l)
#' ## Modify colours, line type and main title
#' plot(res.a, main = "Quercus agrifolia", col = "lightgreen",
#' p.col = "brown4", p.lty = 1)
#' par(opa)
#'
#' @seealso \code{\link{print.htest_boot}} for printing test results,
#' \code{\link{hist}} and \code{\link{abline}} for plotting options,
#' and \code{\link{nestedRanksTest}} for one test that
#' returns an object of class \code{'htest_boot'}
#'
#' @keywords hplot
#'
#' @export
#'
plot.htest_boot <- function(x, breaks, col = "lightblue", border = NA,
digits = getOption("digits"),
main = paste(sep = "", x$method, ", ", x$data.name, "\n",
names(x$statistic), " = ",
format(signif(x$statistic, max(1L, digits - 2L))),
", P = ", format.pval(x$p.value, digits = max(1L, digits - 3L))),
xlab = "Distribution of Z-scores",
ylab = paste(sep = "", "Frequency (out of ", x$n.iter, ")"),
p.col = "red", p.lty = 2, p.lwd = 2, ...)
{
if (is.null(x$null.distribution) || x$n.iter == 1)
stop(deparse(substitute(x)), " does not contain a null distribution")
if (missing(breaks))
breaks <- min(ceiling(x$n.iter / 50), 100)
hist(x$null.distribution, breaks = breaks, col = col, border = border,
main = main, xlab = xlab, ylab = ylab, ...)
abline(v = x$statistic, col = p.col, lty = p.lty, lwd = p.lwd, ...)
}
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