landscape.new.locus: Add a locus

In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description

Add a locus to a Rmetasim landscape object

Usage

## must be called AFTER integer, switch, and float params have been created
landscape.new.locus(rland,type=0,ploidy=1,
             mutationrate=0,transmission=1,numalleles=2,
             allelesize=50,frequencies=NULL, states = NULL)

Arguments

rland	partially created landscape object, required
type	(default=0) type of locus, 0=Infinite Allele mutation model (Integer), 1=Stepwise mutation model (Integer) state, 2=DNA base (variable length string state)
ploidy	(default=1) locus ploidy, 1 or 2
mutationrate	(default=0) probability of mutation per generation, less than or equal to 1
transmission	(default=1) 1=uniparental inheritance, 0=biparental inheritance
numalleles	(default=2) number of different alleles at the time of creation
allelesize	(default=50) length of DNA strings if type=2
frequencies	(default=NULL) vector of frequencies for each allele, must be numalleles long and add up to 1, if NULL frequencies are equally distributed
states	States for each of the alleles specified. If NULL sequential numeric states used.

Examples

  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.locus(exampleland,type=2,ploidy=2,
                          mutationrate=.001,numalleles=5,allelesize=100)

  exampleland$loci

  rm(exampleland)

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