diff_stats: Calculate differentiation statistics for a genind object

In mmod: Modern Measures of Population Differentiation

Description

By default this function calculates three different statistics of differentiation for a genetic dataset. Nei's Gst, Hedrick's G”st and Jost's D. Optionally, it can also calculate Phi'st, which is not calculated by default as it can take somewhat more time to run.

Usage

diff_stats(x, phi_st = FALSE)

Arguments

x	genind object (from package adegenet)
phi_st	Boolean Calculate Phi_st (default is FALSE)

Details

See individual functions (listed below) for more details.

Value

per.locus values for each statistic for each locus in the dataset

global estimtes for these statistics across all loci in the dataset

References

Hedrick, PW. (2005), A Standardized Genetic Differentiation Measure. Evolution 59: 1633-1638.

Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.

Meirmans PG, Hedrick PW (2011), Assessing population structure: FST and related measures. Molecular Ecology Resources, 11:5-18

Nei M. (1973) Analysis of gene diversity in subdivided populations. PNAS: 3321-3323.

Nei M, Chesser RK. (1983). Estimation of fixation indices and gene diversities. Annals of Human Genetics. 47: 253-259.

Meirmans, PW. (2005), Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60: 2399-402.

Excoffier, L., Smouse, P., Quattro, J. (1992), Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-91

See Also

Other diffstat: D_Jost, Gst_Hedrick, Gst_Nei, Phi_st_Meirmans

Examples

data(nancycats)
diff_stats(nancycats)

mmod documentation built on May 1, 2019, 10:55 p.m.