R/fortify.fisherfit.R

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

#' @title Tidied species rank abundance data and estimated Fisher's log-series
#'
#' @description Prepares a data frame of results from a \code{\link{fisherfit}} object suitable for plotting with \code{\link{ggplot}}.
#' @param model an object of class \code{\link{fisherfit}}
#' @param data original data set. Currently ignored.
#' @param ... other arguments pass to methods. Currently ignored.
#' @return A data frame with columns \code{'Rank'} and \code{'Abundance'}. Additionally, Fisher's \eqn{\alpha} and the nuisance parameter are returned as attributes \code{'alpha'} and \code{'k'} respectively.
#'
#' @author Gavin L. Simpson
#'
#' @export
#'
#' @importFrom ggplot2 fortify
#'
#' @examples
#'
#' data(BCI)
#' mod <- fisherfit(BCI[5,])
#' head(fortify(mod))
`fortify.fisherfit` <- function(model, data, ...) {
    df <- data.frame(Rank = as.numeric(names(model[['fisher']])),
                     Abundance = unclass(model[['fisher']]))
    attr(df, 'alpha') <- model[['estimate']]
    attr(df, 'k') <- model[['nuisance']]
    df
}