R/get_satellite.R

In Ebedthan/coremicrobiota: Core Microbiota Analysis

#' Get satellite 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 satellite species
#'
#' @examples
#' df <- data.frame(x = seq(0, 10), y = seq(11, 21))
#' get_satellite(df)
#'
#' @export
get_satellite <- function(x, taxa_are_rows = F) {
  xsad <- sad(x, taxa_are_rows = T)
  return(xsad[xsad$type == "satellite", ])
}