R/taxfac.R

In boydorr/RDiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

#' taxfac
#'
#' @param lookup \code{data.frame} with colnames corresponding to nested
#' hierarchical levels, e.g. c('Species', 'Genus', 'Family', 'Subclass')
#'
#' @noRd
#'
#' @examples
#' \dontrun{
#' # Create Lookup table
#' Species <- c("tenuifolium", "asterolepis", "simplex var.grandiflora", "simplex var.ochnacea")
#' Genus <- c("Protium", "Quararibea", "Swartzia", "Swartzia")
#' Family <- c("Burseraceae", "Bombacaceae", "Fabaceae", "Fabaceae")
#' Subclass <- c("Sapindales", "Malvales", "Fabales", "Fabales")
#' lookup <- cbind.data.frame(Species, Genus, Family, Subclass)
#'
#' taxfac(lookup)
#' }
#'
taxfac <- function(lookup) {
  output <- matrix(ncol = ncol(lookup), nrow = nrow(lookup))
  for (i in seq_len(ncol(lookup)))
    output[, i] <- as.numeric(as.factor(as.character(lookup[, i])))
  row.names(output) <- lookup[, 1]
  colnames(output) <- colnames(lookup)
  output - 1
}