R/rare_abundance.R

In microbiome/microbiome: Microbiome Analytics

#' @title Rare (Non-Core) Abundance Index
#' @description Calculates the rare abundance community index.
#' @inheritParams core_abundance
#' @return A vector of indices
#' @export
#' @examples
#' data(dietswap)
#' d <- rare_abundance(dietswap, detection=0.1/100, prevalence=50/100)
#' @details This index gives the relative proportion of rare
#' species (ie. those that are not part of the core microbiota) in the
#' interval [0,1]. This is the complement (1-x) of the core abundance.
#' The rarity function provides the abundance of the least abundant taxa
#' within each sample, regardless of the population prevalence.
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
#' @seealso core_abundance, rarity, diversity
rare_abundance <- function(x, detection=0.1/100,
    prevalence=50/100, include.lowest = FALSE) {
    
    1 - core_abundance(x, detection, prevalence, include.lowest)
    
}