divMigrate: An experimental function for the detection of directional...

In kkeenan02/diveRsity-dev: Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G'st and In.

Description

divMigrate uses the method described in Sundqvist et al., 2013 to plot the relative migration levels between population samples, from microsatellite allele frequency data. The method is still in the experimental stages, and it is not clear how well it performs under most evolutionary scenarios. Caution should be exercised.

Usage

divMigrate(infile = NULL, stat = "d_jost")

Arguments

infile	Should either be a character string of the input file name or pathway to the input file. This file should be in either the Arlequin genotype file format (.arp), or in the genepop file format.
stat	A character vector of the value stat = 'gst', stat = 'd_jost' (default), or stat = c('gst', 'd_jost'). This argument specifies which statistic should be used to calculate relative migration between samples.

Details

The function will except both Arlequin (.arp) genotype and genepop (.gen/.txt) files, containing co-dominant diploid data. Using the method outlined in Sundqvist et al., 2013, the relative migration levels between all pairs of populations is determined. A weighted network plot is returned, as well as four matrices containing the objects described below.

Value

D_mig	A pairwise matrix containing the normalized relative migration values for all population pairs, as determined by $D_Jost$ values
Gst_mig	A pairwise matrix containing the normalized relative migration values for all population pairs, as determined by $G_ST$ values

Author(s)

Kevin Keenan <[e-mail]>

References

Lisa Sundqvist, M.Z. & Kleinhans, D., 2013. Directional genetic differentiation and asymmetric migration. arXiv pre-print: arXiv:1304.0118v2

Rousset, F., “genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,” Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).

kkeenan02/diveRsity-dev documentation built on May 20, 2019, 10:46 a.m.