divMigrate: An experimental function for the detection of directional...
In diveRsity: A Comprehensive, General Purpose Population Genetics Analysis Package

Description Usage Arguments Details Value Author(s) References

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.

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divMigrate(infile = NULL, outfile = NULL, boots = 0, stat = "all", 
           filter_threshold = 0, plot_network = FALSE, 
           plot_col = "darkblue", para = FALSE)

`infile`	Input genepop file name or path.
`outfile`	String prefix to be added to the results directory. If left `NULL`, no networks will be written to file.
`boots`	The number of bootstrap iteration to carry out for calculating mean relative migration and 95% confidence intervals.
`stat`	A character string indicating which statistic should be used to estimate relative migration between populations. The argument accepts one of the following: "d" (Jost's D), "gst" (Nei's Gst), "Nm" (Alcala et al, 2014) or "all" (all of the preceeding statistics; default).
`filter_threshold`	The minimum relative migration value for which edges in the networks should be displayed.
`plot_network`	A logical argument, specifying whether migration results should be plotted in a network.
`plot_col`	Defines the colour of edges in networks. Default is set to "`darkblue`".
`para`	A logical argument, specifying if multiple CPUs should be used when available.

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.

`Relative migration`	Relative migration matrices
`Significant directional migration`	If `nbs > 0` the significance of pairwise relative migration is tested (i.e. non-overlapping 95% CIs). All non-significant values in the standard relative migration matrices are replaced with 0.

Kevin Keenan <kkeenan02@qub.ac.uk>

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).

Alcala, N., Goudet, J., Vuilleumier, S., 2014, On the transition of genetic differentiation from isolation to panmixia: What we can learn from Gst and D, Theoretical Population Biology, Vol 93, pp75-84.

diveRsity documentation built on May 1, 2019, 10:30 p.m.