diversitySingleLocus: Calculate allelic diversity for a single locus

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

Description

The single argument is, for a single locus, a table of site-by-allele counts, with row names being the site names, and column names being the names given to the individual alleles.

Usage

## S3 method for class 'divtable'
diversitySingleLocus(tab, method = c("r", "q.nielsen",
  "q"), ...)

Arguments

tab	Table of site-by-allele counts, with row names being the site names and column names being the names given to the individual alleles
method	Method to use when calculating diversity within the locus. See diversity.

Details

For specific formulas and discussion of each statistic, see Scofield et al. (2015).

Value

A list of class singlelocus_diversity, containing values returned by diversity or derived from them:

• allele.table, class divtable table of sites by alleles

• allele.N, the total allele count

• allele.G, the number of unique alleles

• allele.q.gg, vector of length number of sites, containing squared frequencies of alleles in each site

• allele.n.g, vector of the number of alleles in each site

• allele.n.k, vector of allele counts for each unique allele

• allele.alpha.g, alpha.g values for each site (EXPAND from diversity)

• allele.q.bar.weighted, weighted mean allele frequency calculated across sites; must this always be an "r" type mean?

• allele.alpha.bar.weighted, reciprocal of allele.q.bar.weighted

• allele.Q.0, reciprocal of allele.gamma

• allele.q.gh, site-by-site matrix of q.gh values across all loci

• allele.overlap, mean site-by-site overlap as calculated by diversity

• allele.divergence, mean site-by-site divergence as calculated by diversity

• allele.gamma, gamma diversity across sites as calculated by diversity

• allele.beta, allele.gamma divided by allele.alpha.bar.weighted

• allele.func.scale.alpha, function for scaling allele.alpha.g and allele.alpha.bar.weighted with given allele.N and allele.G and arbitrary ploidy

• allele.func.scale.gamma, function for scaling allele.gamma with given allele.N and allele.G and arbitrary ploidy

• allele.func.scale.beta, function for scaling allele.beta with given allele.G and arbitrary ploidy

• allele.scaled.ploidy1, a list containing values for allele.alpha.g, allele.alpha.bar.weighted, allele.gamma and allele.beta scaled using the above functions and ploidy of 1

• allele.scaled.ploidy2, a list containing values for allele.alpha.g, allele.alpha.bar.weighted, allele.gamma and allele.beta scaled using the above functions and ploidy of 2

Do we want to generalise allele.q.bar.weighted to compute whatever form of mean is appropriate for method???

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.