Archive/NIMBioS.code/rmetasim/rms.run.R

In christianparobek/skeleSim: Genetic Simulation Engine

rms.run<-function(params){
  sc <- currentScenario(params)
  
  #create rmetasim landscape skeletonland
  skeleland<-rms.init.landscape(
      num.pops = sc@num.pops, carrying = sc@pop.size, mig.rates = sc@migration, 
      num.loc = sc@num.loci, loc.type = sc@locus.type, mut.rate = sc@mut.rate, seq.length = sc@sequence.length, 
      num.stgs = sc@simulator.params@num.stgs, selfing = sc@simulator.params@selfing, 
      surv.matr = sc@simulator.params@surv.matr, repr.matr = sc@simulator.params@repr.matr, 
      male.matr = sc@simulator.params@male.matr,
      init.pop.sizes = sc@simulator.params@init.pop.sizes, 
      num.alleles = sc@simulator.params@num.alleles, allele.freqs = sc@simulator.params@allele.freqs)
  
  #check is landscape ok
  if (!is.landscape(skeleland)) stop("landscape not cool")
  
  #run a number of generations
  skeleland<-landscape.simulate(skeleland, sc@simulator.params@num.gen)

  #take samples
  skeleland_samp<-landscape.sample(skeleland, sc@num.pops, sc@sample.size)
  #print(skeleland_samp)
  
  #now store the results
  params@rep.sample<- rms.convert(skeleland_samp, sc@locus.type)
  return(params)
}