R/prep_data.R

In pnovack-gottshall/ecospace: Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

#' Internal Ecospace Functions.
#'
#' Internal functions not intended to be called directly by users.
#'
#' @param ecospace An ecospace framework (functional trait space) of class
#'   \code{ecospace}.
#' @param Smax Maximum number of species (or other taxa) to include in
#'   simulation.
#'
#' @details Pre-allocate the basic data frame structure so classes (and factor
#'   levels, if used) are properly set. Bit clunky but efficient solution:
#'   adding first placeholder column allows \code{cbind} to work properly with
#'   data frame later, but requires deleting that placeholder at end.
#'
#' @return Returns an empty data frame with pre-defined number of species and
#'   functional traits of proper class type.
#'
#' @seealso \code{\link{create_ecospace}} for how to create an ecospace
#'   framework (functional trait space).
#'
#' @export
prep_data <- function(ecospace, Smax) {
  if (class(ecospace) != "ecospace")
    stop("use create.ecospace() to create a formal ecospace framework.\n")
  pre.data <- as.data.frame(factor(Smax))
  nchar <- length(ecospace) - 1
  seq <- seq_len(nchar)
  state.names <-
    unlist(sapply(seq, function(seq)
      colnames(ecospace[[seq]]$char.space)[seq_len(ncol(ecospace[[seq]]$char.space) - 3)]))
  char.names <- sapply(seq, function(seq)
    ecospace[[seq]]$char)
  cs <-
    sapply(seq, function(seq)
      ncol(ecospace[[seq]]$char.space) - 3)
  for (ch in 1:nchar) {
    if (ecospace[[ch]]$type == "numeric" |
        ecospace[[ch]]$type == "ord.num")
      for (s in seq_len(cs[ch]))
        pre.data <- as.data.frame(cbind(pre.data, numeric(Smax)))
      if (ecospace[[ch]]$type == "factor")
        for (s in seq_len(cs[ch]))
          pre.data <-
            as.data.frame(cbind(
              pre.data, factor(Smax, ordered = FALSE, levels = ecospace[[ch]]$allowed.combos)))
        if (ecospace[[ch]]$type == "ord.fac")
          for (s in seq_len(cs[ch]))
            pre.data <-
              as.data.frame(cbind(
                pre.data, factor(Smax, ordered = TRUE, levels = ecospace[[ch]]$allowed.combos)))
  }
  pre.data <- pre.data[, 2:ncol(pre.data)]
  if (length(char.names) == length(state.names)) {
    colnames(pre.data) <- char.names
  } else {
    colnames(pre.data) <- state.names
  }
  return(pre.data)
}