landscape.setallelefreq: Set Allele frequencies in (a) specific stage(s)

In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description

This function takes a landscape and changes the allele frequencies in different stages based on the list 'af'

Usage

## must be called AFTER landscape has been created and populated
landscape.setallelefreq(rland,af=NULL,states=TRUE)

Arguments

rland	landscape object, required
af	a named list of named lists that specifies states, loci and allele frequencies, see details
states	(default=TRUE) are the alleles specified by state or by allele index (allele indices are stored in the 'individuals' sub-object

Details

The individual initilization function uses a global table of allele frequencies (specified with landscape.new.locus()). This function re-writes the genotypes for specific demographic states and loci with new values. This way it is possible to create demographic state-specifc allele frequency variation.

First the landscape passed to landscape.setpopfreq() must be populated, usually by a call to landscape.new.individuals(). This function cannot be used to add new loci or new alleles to the global system.

This function depends on the data structure 'af' which is a hierarchical set of lists. The highest level in the hierarchy is a named list of demographic state (the first column of the 'individuals' object). Legal values for the names are the integers 0:(number of states-1) then converted to characters. Each element of this list is itself a named list of loci. Legal values for the names are the integers 1:number of loci then converted to characters. Each element of the loci list is a named vector of allele frequencies. The names for these vectors correspond to either: allele states (including DNA sequences) or allele indices (the numbers entered in the 'individuals' subobject as genotypes). The parameter states=TRUE results in the former behavior and states=FALSE, the latter.

Examples

  exampleland <- landscape.new.example()
  af <- list('0'=list('1'=c('1'=0.5,'2'=0.25,'5'=0.25),
                      '2'=c('1'=0.5,'2'=0.25,'3'=0.25)),
             '2'=list('1'=c('1'=0.5,'2'=0.35,'5'=0.15),
                      '2'=c('1'=0.10,'2'=0.15,'3'=0.75)))

  landscape.allelefreq(exampleland)
  landscape.allelefreq(landscape.setallelefreq(exampleland, af))

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