nucleotideDivergence: Nucleotide Divergence

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Nucleotide Divergence

Description

Calculate distributions of between- and within-strata nucleotide divergence (sequence distance), which includes Nei's π (usually referred to as "nucleotide diversity") and Nei's dA between strata.

Usage

nucleotideDivergence(g, probs = c(0, 0.025, 0.5, 0.975, 1), model = "raw", ...)

Arguments

g	a gtypes object.
probs	a numeric vector of probabilities of the pairwise distance distributions with values in 0:1.
model	evolutionary model to be used. see dist.dna for options.
...	other arguments passed to dist.dna.

Value

a list with summaries of the $within and $between strata pairwise distances including Nei's dA (in $between). Nei's π is the mean between-strata divergence.

Author(s)

Eric Archer [e-mail]

References

Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford. (dA: pp. 256, eqn 12.67)

Examples

data(dloop.g)

nd <- nucleotideDivergence(dloop.g)
nd$within
nd$between

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.