rmetasim (version 3.1.14)

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

Description

Extracts locus and allele ids from landscape

Usage

landscape.freq.locnames(Rland)

Arguments

Rland

the Rmetasim landscape object

Value

character vector

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.

See Also

landscape.ind.freq, landscape.make.genind

Examples

# NOT RUN {
  exampleland <- landscape.new.example() 
  exampleland <- landscape.simulate(exampleland, 4)
  landscape.freq.locnames(exampleland)
  rm(exampleland)
# }