R/append_ilr_coords.R

In tystan/deltacomp: Functions to Analyse Compositional Data and Produce Confidence Intervals for Relative Increases and Decreases in the Compositional Components

#' Add ILR coordinates to a data.frame containing composition variables
#'
#' @description Add ILR coordinates to a data.frame containing composition variables
#' @param dataf data.frame containing composition variables
#' @param comps character vector of composition variable names in dataf
#' @param psi ilrBase passed to \code{compositions::ilr()}
#' @export
#' 
# @examples
# library(compositions)
# data(fat_data)
# head(fat_data)
# comp_vars <- c("sl", "sb", "lpa", "mvpa")
# # create sequential binary partition
# sbp <- create_seq_bin_part(length(comp_vars))
# # The orthonormal transformation matrix
# psi <- compositions::gsi.buildilrBase(sbp)
# head(append_ilr_coords(
#   fat_data,
#   comp_vars,
#   psi
# ))



append_ilr_coords <- function(dataf, comps, psi) {

  n <- nrow(dataf)
  n_c <- length(comps)
  ilr_comps <- compositions::ilr(dataf[, comps, drop = FALSE], V = psi)
  if (n == 1) { # special case where "rmult" is a vector not data.frame
    ilr_comps <- as.data.frame(matrix(ilr_comps, nrow = 1))
  } else {
    ilr_comps <- as.data.frame(ilr_comps[1:n, , drop = FALSE])
  }
  ilr_names <- paste0("ilr", 1:(n_c - 1))
  colnames(ilr_comps) <- ilr_names
  
  dataf <- cbind(ilr_comps, dataf)
  return(dataf)

}