R/get.pool.founder.R

In MoBPS: Modular Breeding Program Simulator

'#
  Authors
Torsten Pook, torsten.pook@wur.nl

Copyright (C) 2017 -- 2025  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.
'#

#' Derive founder pool
#'
#' Function to derive the founder pool of individuals
#' @param population Population list
#' @param database Groups of individuals to consider for the export
#' @param gen Quick-insert for database (vector of all generations to export)
#' @param cohorts Quick-insert for database (vector of names of cohorts to export)
#' @param id Individual IDs to search/collect in the database
#' @param use.id Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)
#' @examples
#' data(ex_pop)
#' get.pool.founder(ex_pop, gen=2)
#' @return Founder pool of in gen/database/cohorts selected individuals
#' @export

get.pool.founder <- function(population, database=NULL, gen=NULL, cohorts=NULL, id = NULL, use.id=TRUE){

  database <- get.database(population, gen, database, cohorts, id = id)

  n.animals <- sum(database[,4] - database[,3] +1)
  data <- rep(0, n.animals)
  before <- 0
  names <- numeric(n.animals)
  for(row in 1:nrow(database)){
    animals <- database[row,]
    nanimals <- database[row,4] - database[row,3] +1
    if(nanimals>0){
      data[(before+1):(before+nanimals)] <- population$breeding[[animals[1]]][[36+ animals[2]]][animals[3]:animals[4]]
      names[(before+1):(before+nanimals)] <- paste(if(animals[2]==1) "M" else "F", animals[3]:animals[4],"_", animals[1], sep="")
      before <- before + nanimals
    }
  }

  if(sum(is.na(data))>0){
    unassigned = 0
    per_snp_pool = get.pool(population, database = database)
    for(index in which(is.na(data))){
      activ = as.numeric(per_snp_pool[,c(index*2-1, index*2)])
      if(prod(activ==activ[1])==1){
        data[index] = activ[1]
      } else{
        unassigned = unassigned + 1
      }
    }
    if(unassigned>0){
      warning(paste0(unassigned, " individuals have contributions from multiple pools! No founder pool return for those individuals"))
    }
  }

  if(use.id){
    names(data) <- get.id(population, database = database)
  } else{
    names(data) <- names
  }

  return(data)
}