D_Jost {mmod}

Calculate Jost's D

Description

This function calculates Jost's D from a genind object

Usage

D_Jost(x, hsht_mean = "arithmetic")

Arguments

x

genind object (from package adegenet)

hsht_mean

The type of mean to use to calculate values of Hs and Ht for a global estimate. (Default is teh airthmetic mean, can also be set to the harmonic mean).

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.

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

References

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

See Also

Other diffstat: Gst_Hedrick, Gst_Nei, Phi_st_Meirmans, diff_stats

Other D: pairwise_D

Examples

data(nancycats)
D_Jost(nancycats)
D_Jost(nancycats, hsht_mean= "arithmetic")