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strataG (version 2.4.905)

popStructStat: Population structure statistics

Description

Population structure statistics

Usage

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

Arguments

g

a '>gtypes object.

nrep

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

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 "hedrick" or "nei".

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, statFis

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

statFst

Weir, B. and Cockerham, C. 1984. Estimating F-Statistics for the Analysis of Population Structure. Evolution 38(6):1358-1370. doi:10.2307/2408641

statGst, statGstPrime

Nei, M. 1973. Analysis of gene diversity in subdvidided populations. Proc. Nat. Acad. Sci. 70(12):3321-3323. Hedrick, P.W. 2005. A standardized genetic differentiation measure. Evolution 59(8):1633-1638.

statFstPrime, statGstDblPrime

Miermans, P.G. and P.W. Hedrick. 2011. Assessing population structure: FST and related measures. Molecular Ecology Resources 11:5-18.

statJostD

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

statPHIst

Excoffier, L., P.E. Smouse, and J.M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479-491.