R/fortify.poolaccum.R

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

#' @title Fortify extrapolated species richness of a species pool
#'
#' @description Prepares a fortified version of results from
#'   [vegan::poolaccum()] objects.
#'
#' @param model an object of class [vegan::poolaccum()].
#' @param data original data set. Currently ignored.
#' @param alpha level of quantiles for envelopes shown (default 0.05).
#' @param ... additional arguments passed to [vegan::summary.poolaccum()],
#'   notably `display` to control which indices should be computed.
#'
#' @return A data frame with columns `index`, `size`, `richness`, `lower`,
#'   `upper`, and `std_dev`, containing the richness index, permutation richness
#'   estimator, sample size, upper and lower \eqn{1 - \alpha}{1 - alpha}
#'   quantile interval, and standard deviation of permutation estimates,
#'   respectively.
#'
#' @export
#'
#' @importFrom ggplot2 fortify
#'
#' @author Didzis Elferts & Gavin L. Simpson
#'
#' @examples
#' data(BCI)
#' pool <- poolaccum(BCI)
#' df <- fortify(pool)
#'
#' ggplot(df, aes(x = size, y = richness, colour = index)) +
#'     geom_ribbon(aes(ymin = lower, ymax = upper, x = size, fill = index),
#'                 alpha = 0.3, inherit.aes = FALSE) +
#'     geom_line() +
#'     facet_wrap(~ index)

`fortify.poolaccum` <- function(model, data, alpha = 0.05, ...) {
    m <- summary(model, alpha = alpha, ...)
    lens <- vapply(m, NROW, numeric(1), USE.NAMES = FALSE)
    vars <- vapply(m, function(x) colnames(x)[2], character(1),
                   USE.NAMES = FALSE)
    df <- as.data.frame(do.call("rbind", m)) # bind_rows later?
    names(df) <- c("size", "richness", "lower", "upper", "std_dev")
    df <- cbind(index = factor(rep(vars, times = lens)), df)
    df
}