landscape.new.individuals: Fill a landscape with individuals

In stranda/rmetasim: An Individual-Based Population Genetic Simulation Environment

Fill a landscape with individuals

Description

Create a set of individuals for a Rmetasim landscape object.

Usage

  ## must be called AFTER integer, switch, and float params, demography,
  ## epochs, and loci have been created

   landscape.new.individuals(rland,PopulationSizes)

Arguments

rland	nearly complete landscape object, required
PopulationSizes	vector of integers denoting how many individuals are in which stage and in which subpopulation, vector is ordered as: (pop1 stage1, pop1 stage2, ..., pop2 stage1, pop2stage2, ....), must be of length rland$intparam$habitats * rland$intparam$stages

Examples

  
  exampleS <- matrix(c(0.1, 0, 0.5, 0.3), nrow = 2)
  exampleR <- matrix(c(0, 1.1, 0, 0), nrow = 2)
  exampleM <- matrix(c(0, 0, 0, 1), nrow = 2)
  
  exampleland <- landscape.new.empty()
  exampleland <- landscape.new.intparam(exampleland, s=2, h=2)
  exampleland <- landscape.new.floatparam(exampleland)
  exampleland <- landscape.new.switchparam(exampleland)
  exampleland <- landscape.new.local.demo(exampleland,exampleS,exampleR,exampleM)

  ## nonsense matricies
  exampleS <- matrix(c(rep(0,4),
                rep(1,4),
                rep(0,4),
                rep(1,4)), nrow = 4)
  exampleR <- matrix(c(rep(0.5,4),
                rep(0,4),
                rep(0.5,4),
                rep(0,4)), nrow = 4)
  exampleM <- matrix(c(rep(0,4),
                rep(.25,4),
                rep(0,4),
                rep(0,4)), nrow = 4)

  exampleland<- landscape.new.epoch(exampleland,exampleS,exampleR,exampleM)
  exampleland <- landscape.new.locus(exampleland,type=2,ploidy=2,
                   mutationrate=.001,numalleles=5,allelesize=100)
  exampleland <- landscape.new.locus(exampleland,type=1,ploidy=1,mutationrate=.001,numalleles=3)
  exampleland <- landscape.new.locus(exampleland,type=0,ploidy=2,mutationrate=.004,numalleles=4)

  exampleland <- landscape.new.individuals(exampleland,
                 c(5,20,7,15))

  exampleland$individuals

  rm(exampleS)
  rm(exampleR)
  rm(exampleM)
  rm(exampleland)

stranda/rmetasim documentation built on Aug. 25, 2023, 12:22 p.m.