landscape.freq.locnames: Return a vector of locus IDs concatenated to Allele ids

In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description

Extracts locus and allele ids from landscape

Usage

  landscape.freq.locnames(Rland)

Arguments

Rland

the Rmetasim landscape object

Details

This function returns a vector of reasonable column names for a frequency by individual matrix from an Rland object. It is mainly useful in creating genind objects from landscapes.

Genotypes are stored in a landscape object as columns representing allelic position. If the locus is haploid, there is a single column and if diploid, two. The allele indices are entered in each column for individual genotypes.

The 'frequency per individual' format has a column for every locusXallele combination; genotypes are represented as the frequency of particular alleles in an individuals genotype (for example freq = 1 in a column diploid means that the individual is homozygous for that column, 0.5 in two columns represents a heterozygote for the alleles represented by those two columns). This is essentially the genind format from adegenet.

Value

character vector

See Also

landscape.ind.freq, landscape.make.genind

Examples

  exampleland <- landscape.new.example() 
  exampleland <- landscape.simulate(exampleland, 4)
  landscape.freq.locnames(exampleland)
  rm(exampleland)

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