R/miraculix.R

In MoBPS: Modular Breeding Program Simulator

'#
  Authors
Torsten Pook, torsten.pook@uni-goettingen.de

Copyright (C) 2017 -- 2020  Torsten Pook

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
'#

#' Add miraculix-coding for genotypes
#'
#' Internal function to store genotypes bit-wise
#' @param population Population list
#' @return Population list
#' @examples
#' # This is only relevant with the package miraculix is installed and used
#' population <- creating.diploid(nsnp=100, nindi=50, miraculix=FALSE)
#' \donttest{population <- miraculix(population)}
#' @export

miraculix <- function(population){

  if (requireNamespace("miraculix", quietly = TRUE)) {
    if(population$info$miraculix){
      warning("Miraculix is already active. Why do you use this function?")
      return(population)
    } else{
      population$info$miraculix <- TRUE
    }

    for(gen in 1:length(population$breeding)){
      for(sex in 1:2){
        if(length(population$breeding[[gen]][[sex]])){
          for(nr in 1:length(population$breeding[[gen]][[sex]])){

            if(length(population$breeding[[gen]][[sex]][[nr]][[9]])>0){
              genotype <- cbind(population$breeding[[gen]][[sex]][[nr]][[9]], population$breeding[[gen]][[sex]][[nr]][[10]] )
              population$breeding[[gen]][[sex]][[nr]][[9]] <- miraculix::haplomatrix(genotype)
              population$breeding[[gen]][[sex]][[nr]][[10]] <- "Placeholder_Pointer_Martin"
            }
          }
        }

      }
    }
  } else{
    warning("miraculix is not available! No conversion possible")

  }

  return(population)

}