Calculate Jost's D

Usage

D_Jost(x)

Arguments

x
genind object (from package adegenet)

Value

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

global estimtes for D based on overall heterozygosity or the harmonic mean of values for each locus

Description

This function calculates Jost's D from a genind object

Details

Takes a genind object with population information and calculates Jost's D Returns a list with values for each locus as well as two global estimates. 'global.het' uses the averages of Hs and Ht across all loci while 'global.harm_mean' takes the harmonic mean of all loci.

Because estimators of Hs and Ht are used, its possible to have negative estimates of D. You should treat these as numbers close to zero.

References

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

Examples

data(nancycats) D_Jost(nancycats)
$per.locus fca8 fca23 fca43 fca45 fca77 fca78 fca90 0.42006021 0.23738411 0.21319208 0.14335289 0.42300076 0.13147655 0.31183460 fca96 fca37 0.30740024 0.09737005 $global.het [1] 0.2350486 $global.harm_mean [1] 0.2001798

See also

Other D: pairwise_D Other diffstat: Gst_Hedrick, Gst_Nei, Phi_st_Meirmans, diff_stats