R/read_archfile.R

In rscherrer/EGS:

#' Read an architecture file
#'
#' @param filename Path to the architecture file
#'
#' @export

read_archfile <- function(filename) {

  archfile <- read.delim(filename, header = FALSE)[, 1]

  begin <- grep("^Architecture:$", archfile)
  if (length(begin) == 0) stop(paste0("Cannot find the beginning of the genetic architecture in file ", filename))
  begin <- begin + 1
  archfile <- archfile[begin:length(archfile)]

  fields <- c("chromosomes", "traits", "locations", "effects", "dominances")
  arch <- lapply(fields, function(x) str2vec(archfile[which(archfile == x)[1] + 1]))
  names(arch) <- fields

  ii <- grep("network", archfile)
  networks <- lapply(ii, function(i) list (
    edges0 = str2vec(archfile[i + 2]),
    edges1 = str2vec(archfile[i + 4]),
    weights = str2vec(archfile[i + 6])
  ))
  names(networks) <- c("ecotrait", "matepref", "neutral")
  arch$networks <- networks

  return (arch)

}