R/autoplot.fisherfit.R

In gavinsimpson/ggvegan: 'ggplot2' Plots for the 'vegan' Package

#' @title Plot Fisher's log-series
#'
#' @description Draws a bar plot of species rank abundance with Fisher's log-series superimposed.
#'
#' @param object an object of class \code{\link{fisherfit}}.
#' @param show.fitted logical; should the estimated distribution also be plotted?
#' @param xlab character; label for the x axis.
#' @param ylab character; label for the y axis.
#' @param title character; subtitle for the plot.
#' @param subtitle character; subtitle for the plot.
#' @param caption character; caption for the plot.
#' @param bar.col colour for the bar outlines. The default, \code{NA}, does not draw outlines around bars.
#' @param bar.fill fill colour for the bars.
#' @param line.col colour for Fisher's log-series curve.
#' @param size numeric; size aesthetic for the log-series curve.
#' @param ... additional arguments passed to other methods.
#' @return A ggplot object.
#' @author Gavin L. Simpson
#'
#' @export
#'
#' @importFrom ggplot2 ggplot autoplot geom_bar stat_function aes_string labs fortify
#'
#' @examples
#'
#' data(BCI)
#' mod <- fisherfit(BCI[5,])
#' autoplot(mod)
`autoplot.fisherfit` <- function(object, show.fitted = TRUE,
                                 xlab = "Abundance", ylab = "Number of Species",
                                 title = "Fisher's log-series distribution",
                                 bar.col = NA, bar.fill = "grey35",
                                 line.col = "red", size = 1,
                                 subtitle = NULL, caption = NULL,
                                 ...) {
    fishfun <- function(x, k, alpha) {
        alpha * k^x / x
    }
    df <- fortify(object)
    plt <- ggplot(df, aes_string(x = 'Rank', y = 'Abundance')) +
        geom_bar(stat = 'identity', colour = bar.col, fill = bar.fill)
    if (show.fitted) {
        alpha <- object[['estimate']]
        k <- object[['nuisance']]
        plt <- plt + stat_function(fun = fishfun, args = list(k = k, alpha = alpha),
                                   colour = line.col, size = size)
    }
    plt <- plt + labs(x = xlab, y = ylab, title = title, subtitle = subtitle,
                      caption = caption)
    plt
}