R/standardise_comps.R

In codaredistlm: Compositional Data Linear Models with Composition Redistribution

standardise_comps <- function(dataf, comps) {

  # standardise comps
  comp_totals <- rowSums(dataf[, comps])
  comps_to_use <- compositions::acomp(dataf[, comps])

  message("---\nThese are the quartiles of the summed compositions:\n")
  message(paste(kable(quantile(comp_totals, seq(0, 1, by = 0.25))), collapse = "\n"))
  message("---\n")
  dataf[, comps] <- as.data.frame(comps_to_use)

  ## equally could use: dataf[, comps] / matrix(comp_totals, ncol = n_comp, nrow = n)
  # i.e.,note that these are equal
  # as.data.frame(compositions::acomp(dataf[,comps])) -
  # dataf[, comps] / matrix(comp_totals, ncol = n_comp, nrow = n)

  return(dataf)

}