R/rare_members.R

In microbiome/microbiome: Microbiome Analytics

#' @title Rare Taxa
#' @description Determine members of the rare microbiota with given abundance
#' and prevalence threshold.
#' @inheritParams core
#' @return Vector of rare taxa
#' @details For phyloseq object, lists taxa that are less prevalent than the
#' given prevalence threshold. Optionally, never exceeds the given abundance
#' threshold (by default, all abundaneces accepted). For matrix, lists
#' columns that satisfy these criteria.
#' @examples
#' data(dietswap)
#' # Detection threshold: the taxa never exceed the given detection threshold
#' # Prevalence threshold 20 percent (strictly greater by default)
#' a <- rare_members(dietswap, detection=100/100, prevalence=20/100)
#' @seealso core_members
#' @export
#' @references
#' To cite the microbiome R package, see citation('microbiome') 
#' @author Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
rare_members <- function(x, detection=1/100, prevalence=50/100,
    include.lowest = FALSE) {
    
    # Pick core taxa 
    cm <- core_members(x, detection = detection,
                        prevalence = prevalence, 
                        include.lowest = include.lowest)

    # Take complement
    taxa <- setdiff(taxa(x), cm)

    # Return
    taxa
    
}