metrics: Population genetic metrics

In jmsigner/fpga: fast population genetic analysis

Description

Functions to calculate population genetic metrics. For all functions stratum splits the data set into different populations. If stratum is missing, one population is assumed. n_alls returns the number of alleles per population. rarify rarifies a population genetic metric.

Usage

freq(x, stratum)

het_obs(x, stratum)

het_exp(x, stratum)

n_alls(x, stratum)

n_eff_alls(x, stratum)

nprivate_alleles(x, stratum)

rarify(x, FUN, stratum, nperm = 100)

Arguments

x	Three dimensional array with individuals, loci and alleles in the first, second and third dimension.
stratum	Vector of length nrow(x) indicating population membership.
FUN	Function to rarify.
nperm	Number of permutations.

jmsigner/fpga documentation built on May 19, 2019, 1:56 p.m.