landscape.new.individuals: Fill a landscape with individuals

In stranda/kernelPop2: Spatially explicit population genetic simulations

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

  rland <- 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/kernelPop2 documentation built on March 30, 2020, 5:37 a.m.