R/speciesTable.R

In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

#' Customize species trait table values
#'
#' @param speciesTable The species traits table
#' @param params       A named list (of parameters) of named lists (by species), with species
#'                     traits overrides (e.g., \code{list(seeddistance_eff = list(Abie_sp = 25))}).
#'
#' @author Alex Chubaty and Ceres Barros
#' @export
updateSpeciesTable <- function(speciesTable, params) {
  ## checks:
  traits <- names(params)
  missingTraits <- traits[!traits %in% names(speciesTable)]
  if (length(missingTraits))
    stop("The traits: ", paste(missingTraits, collapse = ", "), "\ndo not exist in `speciesTable`")

  for (trt in traits) {
    subParams <- params[[trt]]

    ## checks:
    spp <- names(subParams)
    missingSpp <- spp[!spp %in% speciesTable$species]
    if (length(missingSpp))
      stop("The species: ", paste(missingSpp, collapse = ", "),
           "\ndo not exist in `speciesTable$species`")

    ## this is sub ideal to convert classes, but the only solution I found.
    ## neither class(...) <- class(..) nor as(..., class(...)) were changing integer to numeric.
    ## only as.numeric(...) worked
    if (class(unlist(subParams)) != class(speciesTable[[trt]])) {
      asFUN <- get(paste0("as.", class(unlist(subParams))))
      if (!is.function(asFUN))
        stop("Can't find an `as.` method to convert class to '", class(unlist(subParams)), "'")

      speciesTable <- speciesTable[, (trt) := lapply(.SD, asFUN), .SDcols = trt]
    }

    for (sp in spp) {
      set(speciesTable, which(speciesTable$species == sp), trt, subParams[[sp]])
    }
  }

  return(speciesTable)
}