R/summarise.R

In boydorr/RDiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

#' Summary function
#'
#' This function converts columns of an array (each representing community
#' counts) into proportions, so that each column sums to 1.
#'
#' @param populations An S x N array whose columns are counts of individuals.
#' @param normalise Normalise probability distribution to sum to 1 for each
#' column rather than just along each set.
#'
#' @return Returns an array whose columns are proportions.
#'
#' @noRd
#'
summarise <-
  function(populations, normalise = TRUE) {
    totals <- array(rowSums(populations), dim = c(dim(populations)[1], 1))

    if (normalise) {
      total <- sum(totals)
      totals <- totals / total
      proportions <- populations / total
      weights <- colSums(proportions)
      proportions <- proportions %*% diag(1 / (weights))
    } else {
      proportions <- populations
      weights <- colSums(proportions)
    }
    num <- length(weights)

    list(proportions = proportions, totals = totals,
         weights = array(weights, dim = c(1, num)), num = num)
  }