R/low_abundance.R

In microbiome/microbiome: Microbiome Analytics

#' @title Low Abundance Index
#' @description Calculates the concentration of low-abundance taxa below the
#' indicated detection threshold.
#' @inheritParams core
#' @return A vector of indicators.
#' @export
#' @examples
#' data(dietswap)
#' d <- low_abundance(dietswap, detection=0.2/100)
#' @details The low_abundance index gives the concentration of species at low
#' abundance, or the  relative proportion of rare species in [0,1].
#' The species that are below the indicated detection threshold are
#' considered rare. Note that population prevalence is not considered.
#' If the detection argument is a vector, then a data.frame is returned,
#' one column for each detection threshold.
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
#' @seealso core_abundance, rarity, global
low_abundance <- function(x, detection=0.2/100) {
    
    if (length(detection) > 1) {
        tab <- vapply(detection, function(th) {
            low_abundance(x, detection=th)
        }, 1)
        colnames(tab) <- as.character(detection)
        rownames(tab) <- colnames(abundances(x))
        return(tab)
    }
    
    xc <- abundances(x, transform="compositional")
    do <- apply(xc, 2, function(x) {
        sum(x[x < detection])
    })
    names(do) <- colnames(x)
    
    do
    
}