landscape.new.epoch.step {rmetasim}R Documentation

Create a stepping-stone migration model

Description

Create an epoch for a Rmetasim landscape object that follows the conventions of island migration models where all populations exchange migrants at equal rates

Usage

  ## must be called AFTER integer, switch, and float params have
  ## been created and after the demography has been created

  rland <- landscape.new.epoch.step(rland,s,sfrom,sto,m,mfrom,mto,f,ffrom,fto,
                            epochprob=1,startgen=0,extinct=NULL,carry=NULL,localprob=NULL)

Arguments

rland partially created landscape object, required
s Rate of migration by individuals
sfrom vector of lifecycle stages in which the individuals migrate from their current subpopulation, must be rland$intparam$stages in length
sto vector of lifecycle stages in which the individuals arrive in a new subpopulation, must be rland$intparam$stages in length
m Rate of migration by newborns
mfrom vector of lifecycle stages in which the newborns leave their subpopulation, must be rland$intparam$stages in length
mto vector of lifecycle stages in which the newborns arrive at their new subpopulation, must be rland$intparam$stages in length
f Rate of sperm/pollen movement
ffrom vector of lifecycle stages in which the males produce sperm/pollen, must be rland$intparam$stages in length
fto ???
epochprob (default=1) probability of choosing this epoch randomly if randepoch==1
startgen (default=0) generation in which this epoch starts
extinct (default=NULL) vector of extinction probabilities per generation for each subpopulation, must be rland$intparam$habitats in length, passing NULL gives a 0% probability of extinction to each subpopulation
carry (default=NULL) vector of carrying capacities for each subpopulation, must be rland$intparam$habitats in length, passing NULL gives a 1000 individual carrying capacity to each subpopulation
localprob (default=NULL) vector of probabilites for choosing local demographies, must be length(rland$demography$localdem) in length, passing NULL gives each demography an equal probability

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)

  exampleland <- landscape.new.epoch.island(exampleland,.1,c(0,1),c(0,1),.3,c(0,1),c(1,0),.5,c(1,0),c(0,1))

  exampleland$demography$epochs[[1]]

  rm(exampleland)

[Package rmetasim version 1.1.008 Index]