landscape.new.epoch: Create an Epoch

In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description

Create an epoch for a Rmetasim landscape object

Usage

  ## must be called AFTER integer, switch, and float params have
  ##   been created and after the demography has been created
  ## S, R, and M matricies must be square matricies of size X by X
  ##   where X = rland$intparam$stages*rland$intparam$habitats

landscape.new.epoch(rland,S=NULL,R=NULL,M=NULL,
epochprob=1,startgen=0,extinct=NULL,carry=NULL,
localprob=NULL)

Arguments

rland	partially created landscape object, required
S	(default=NULL) Survivablity matrix for epoch, NULL gives no movement between subpopulations (0 matrix)
R	(default=NULL) female Reproduction matrix for epoch, NULL gives no dispersal between subpopulations (0 matrix)
M	(default=NULL) Male reporduction matrix for epoch, NULL gives no sperm or pollen movement between subpopulations (0 matrix)
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)

  ## 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)

  ## defaults
  exampleland<- landscape.new.epoch(exampleland,exampleS,exampleR,exampleM)

  exampleland$demography$epochs[[1]]

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

rmetasim documentation built on Feb. 8, 2020, 1:06 a.m.