recluster.fst.pair: Compute pairwise indexes of genetic differentiation among...
In recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Description Usage Arguments Details Value Author(s) References Examples

This function computes pairwise indexes of genetic differentiation among populations based on a distance matrix and on a vector for populations.

1	recluster.fst.pair(dist,vect,setzero=F,setnazero=F)

`dist`	A distance matrix.
`vect`	A vector indicating population membership. Cases must be in the some order of the distance matrix.
`setzero`	A logical indicating if negative values should be set to zero
`setnazero`	A logical indicating if NA values should be set to zero

The formulas used for pairwise calculations between i and j populations are Dstij = Htij - Hsij Gstij = Dstij/Ht Dij = (Dstij/(1-Hsij))*2 G'stij = Gstij/((1-Hsij)/(1+Hsij)) see also recluster.fst for a discussion of indexes

`Dstm`	The Dst distance matrix.
`Gstm`	The Gst distance matrix.
`Dm`	The D distance matrix.
`G1stm`	The G'st distance matrix.

Leonardo Dapporto

Jost L. "GST and its relatives do not measure differentiation." Mol Ecol (2008), 17:4015-4026.

Meirmans P. G., Hedrick P. W. "Assessing population structure: FST and related measures: Invited Technical Reviwev." Mol Ecol Res (2011), 11: 5-18.

Nei M. Molecular evolutionary genetics (1987), Columbia University Press.

Whitlock M.C. "G'ST and D do not replace FST." Mol Ecol (2011), 20: 1083-1091.

datavirtual<-data.frame(replicate(20,sample(0:1,60,rep=TRUE)))
dist<-recluster.dist(datavirtual)
population<-c(rep(1,20),rep(2,20),rep(3,20))
recluster.fst.pair(dist,population)