R/mutation.R

In zhrlin/GA: What the Package Does (One Line, Title Case)

#' Mutation
#'
#' @description \code{mutation} is to do mutation for the offspring after breeding.
#' @param parent_1,parent_2 Numeric vectors with binary 0/1 elements. Should be of same length.
#' @param offspring A Numeric vector generated by \code{crossover} and/or other genetic operators.
#' @param m Mutation rate: a numeric value between 0 and 1. By default 0.01.
#' @details Changes an offspring chromosome by randomly introducing one or
#' more alleles in loci where those alleles are not seen in the
#' corresponding loci of either parent chromosome.


mutation <- function(parent_1, parent_2, offspring, m) {

  ## test whether there are missing arguments
  assert_that(!is.null(parent_1) && !is.null(parent_2) && !is.null(offspring) && !(is.null(m)))
  # test whether the inputs are numeric vectors
  assert_that(is.numeric(parent_1), is.numeric(parent_2), is.numeric(offspring))
  ## test whether the length of two chromosomes are the same
  assert_that(length(parent_1) == length(parent_2))


  same <- sum(parent_1 == parent_2)
  # two parents have some same genes
  if (same != 0) {
    same_loci <- which(parent_1 == parent_2)
    # alternate the gene 0 to 1 or 1 to 0 with probability m
    mutated_offspring = sapply(same_loci, function(x) {
      # mutate
      if (runif(1) < m) {
        return(1-offspring[x])
      }
      return(offspring[x])
    })

    offspring[same_loci] <- mutated_offspring
  }


  ## test for the two parents without same genes, offspring unchanged
  return(offspring)
}