R/tidy_beta_multi_abund.R

In PaulESantos/tidyversity: Tidy version of betapart(1.5.0)

#' tidy_beta_multi_abund
#'
#' Representacion grafica de las matrices de disimilaridad resultado de
#' la funcion "beta.pair". Visualizacion grafica de Turnover y Nestedness.
#'
#'
#' @param x matriz de p/a o abundancia de especies.
#' @param index.family pude trabajar con "bray" o "ruzicka".
#' @return A data_frame.
#' @export
#'
tidy_beta_multi_abund <- function (x, index.family = "bray")
{requireNamespace("tidyverse")
  requireNamespace("betapart")
  index.family <- match.arg(index.family, c("bray", "ruzicka"))
  if (!inherits(x, "betapart.abund")) {
    x <- betapart::betapart.core.abund(x)
  }
  maxbibj <- sum(x$pair.max.not.shared.abund)
  minbibj <- sum(x$pair.min.not.shared.abund)
  switch(index.family, bray = {
    beta.bray.bal <- minbibj/(minbibj + x$multiple.shared.abund)
    beta.bray.gra <- (x$multiple.shared.abund/(minbibj +
                                                 x$multiple.shared.abund)) * ((maxbibj - minbibj)/((2 *
                                                                                                      x$multiple.shared.abund) + maxbibj + minbibj))
    beta.bray <- (minbibj + maxbibj)/(minbibj + maxbibj +
                                        (2 * x$multiple.shared.abund))
    multi <- dplyr::data_frame(beta.BRAY.BAL = beta.bray.bal, beta.BRAY.GRA = beta.bray.gra,
                        beta.BRAY = beta.bray)
  }, ruzicka = {
    beta.ruz.bal <- (2 * minbibj)/((2 * minbibj) + x$multiple.shared.abund)
    beta.ruz.gra <- (x$multiple.shared.abund/((2 * minbibj) +
                                                x$multiple.shared.abund)) * ((maxbibj - minbibj)/((x$multiple.shared.abund) +
                                                                                                    maxbibj + minbibj))
    beta.ruz <- (minbibj + maxbibj)/(minbibj + maxbibj +
                                       x$multiple.shared.abund)
    multi <- dplyr::data_frame(beta.RUZ.BAL = beta.ruz.bal, beta.RUZ.GRA = beta.ruz.gra,
                        beta.RUZ = beta.ruz)
  })
  return(multi)
}