strataG (version 2.0.2)

popStructStat: Population structure statistics

Description

Population structure statistics

Usage

Hstats(g)
statChi2(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statFis(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statFst(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statFstPrime(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statGst(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statGstPrime(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE,
  prime.type = c("nei", "hedrick"), ...)
statGstDblPrime(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statJostD(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE, ...)
statPhist(g, nrep = NULL, strata.mat = NULL, keep.null = FALSE,
  model = "K80", gamma = FALSE, pairwise.deletion = TRUE, ...)

Arguments

g

a '>gtypes object.

nrep

number specifying number of permutation replicates to use for permutation test.

strata.mat

an optional matrix of permuted stratifications. See Notes for more details. Ignored if nrep is not NULL.

keep.null

logical. Keep the null distribution from the permutation test?

...

optional arguments passed to or from other functions.

prime.type

type of G'st to calculate. Can be "nei" or "hedrick".

model, gamma, pairwise.deletion

parameters passed to dist.dna. Note that defaults for these arguments (in particular model) are the same as in dist.dna.

Value

A list with three elements:

stat.name

the name of the statistic.

result

a vector of the statistic estimate and the p-value, if replicates were conducted.

null.dist

a vector of the null distribution from the permutations.

References

Hstats

Nei, M. and R.K. Chesser. 1983. Estimation of fixation indices and gene diversities. Ann. Hum. Genet. 47:253-259.