R/mut.R

In drizztxx/gatbxr: Genetic Algorithm Toolbox Implemented by R

#' @title MUTATion low-level function
#'
#' @description
#' This function takes the representation of the current population,
#' mutates each element with given probability and returns the resulting
#' population.
#'
#' @usage 
#' mut(OldChrom,Pm=NULL,BaseV=NULL)
#'
#' @param OldChrom a matrix containing the chromosomes of the
#' current population. Each row corresponds to
#' an individuals string representation.
#' @param Pm a value indicating mutation probability. Default value
#' of Pm = 0.7/Lind, where Lind is the chromosome length.
#' @param BaseV	an optional vector of the same length as the
#' chromosome structure defining the base of the 
#' individual elements of the chromosome. Default is set to binary
#' representation.
#'
#' @return
#' a matrix containing a mutated version of OldChrom.
#' @export
#' @author 
#' The original matlab implementation of mutate was written by Andrew Chipperfield.
#' The R implementation was written by David Zhao. 
#' @examples
#' 
#' Chrom = crtbp(40,10)$Chrom
#' 
#' NewChrom = mut(OldChrom=Chrom)

mut <- function(OldChrom,
                Pm=NULL,
                BaseV=NULL){
  ## get population size (Nind) and chromosome length (Lind)
  Nind <- NROW(OldChrom);Lind <- NCOL(OldChrom)
  
  ## check input parameters
  if(is.null(Pm)) Pm <- 0.7/Lind
  if(is.null(BaseV)) BaseV <- crtbase(Lind)
  
  if(Lind != length(BaseV)) stop("OldChrom and BaseV are incompatible")
  
  ## create mutation mask matrix
  BaseM <- matrix(rep(1,Nind)) %*% BaseV
  
  ## perform mutation on chromosome structure
  Mask <- (matrix(runif(Nind*Lind),Nind,Lind)<
             Pm)*ceiling(matrix(runif(Nind*Lind),Nind,Lind)*(BaseM-1))  
  NewChrom <- (OldChrom+Mask) %% BaseM
  
  return(NewChrom)
}