COR_Fstd: Function for calculating pairwise Fst and correlation...
In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Description Usage Arguments Details Value Author(s) References See Also Examples

This function calculates pairwise genetic differentiation (Fst), as well as the correlation coefficient between genetic differentiation (Fst) and geographic distance.

1	COR_Fstd(x, d, ncode,nrepet)

`x`	A genetic data files, here the format is genepop format.
`d`	Pairwise geographic distance for calculating correlations. If no actual geographic distance, d=NULL. The geographic distance should be a matrix that corresponds to the pairwise genetic differentiation matrix.
`ncode`	The code type of the genotype.
`nrepet`	Number of permutations.

This function returns lists of pairwise Fst matrix, and a matrix of theorical geographical distance if d is NULL, as well as the correlation coefficient.

`pwFst`	The pairwise genetic differentiation (Fst) matrix.
`COR_Fstd`	Pearson correlation coefficient between genetic differentiation (Fst) and geographic distance.

qinxinghu@gmail.com

Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5(1), 184-186.

Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24 (11), 1403-1405.

Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.

Weir B.S. and Cockerham C.C. (1984) Estimating F-Statistics for the Analysis of Population Structure. Evolution 38:1358

Evolution and the Genetics of Populations Volume 2: the Theory of Gene Frequencies, pg 294-295, S. Wright, Univ. of Chicago Press, Chicago, 1969.

COR_detaDd

# example genepop file, the example file is a complicated hierarchical island model
f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
#d2=COR_Fstd(infile,d=NULL,ncode=3,nrepet=999)
#print(d2)