R/get_core.R

In Ebedthan/coremicrobiota: Core Microbiota Analysis

#' Get core microbiota based on ASV Poisson modelling
#'
#' @param x A data frame representing a ASV/OTU table with raw counts or
#'          phyloseq object.
#'
#' @param taxa_are_rows A logical indicating if OTU are rows
#'
#' @return A data frame of species abundance distribution of core microbiome.
#'
#' @examples
#' df <- data.frame(x = seq(0, 10), y = seq(11, 21))
#' get_core(df)
#'
#' @export
get_core <- function(x, taxa_are_rows = F) {
  xsad <- sad(x, taxa_are_rows = taxa_are_rows)
  return(xsad[xsad$type == "core", ])
}