rmetasim (version 3.1.14)

landscape.new.individuals: 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

# NOT RUN {
  
  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)
# }