popStructStat: Population structure statistics

In strataG: Summaries and Population Structure Analyses of Genetic Data

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.

Note

If strata.mat is provided, it must be a numeric matrix of integers from 0 to k - 1, where k is the number of strata. Each column is a separate permutation and the first column is assumed to represent the original stratification. If not provided (strata.mat = NULL), stratification is taken from g. This argument is primarily used internally by popStructTest.

Author(s)

Eric Archer [e-mail]

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.

strataG documentation built on Feb. 28, 2020, 9:07 a.m.