[R-sig-genetics] Nei-Li distance

[gmail]

Hi all,
here is the function to calculate Nei-Li (1979) distance (or 
dissimilarity) for a binary matrix where columns are species and rows 
are alleles.
It is a modification of "jaccard" function in package prabclus by 
Christian Hennig and Bernhard Hausdorf.

########################################
neidist<-function (regmat)
{
    nart <- ncol(regmat)
    jdist <- rep(0, nart * nart)
    dim(jdist) <- c(nart, nart)
    reg.col.sum <- apply(regmat, 2, sum)
    reg.aggrement <- t(regmat) %*% regmat
    nedist <- 1 - (reg.aggrement+reg.aggrement)/((reg.col.sum - 
t(t(reg.aggrement) -
        reg.col.sum))+reg.aggrement)
    nedist
}
###############################################


Useful in AFLP or other dominant (0-1 response) markers analysis

Fiorello Toneatto