standard variation in dissimilarity matrix

Dear all,
linked to MRPP in Vegan there is a really nice function (meandist)
which calculates a matrix of mean of distance, based on a grouping
factor, from matrices of dissimilarity. I was wondering if there is an
equivalent function calculating the standard deviation instead of the
mean distance or if anyone has an idea how to do it.
thanks a lot!
Magali

meandist() computes the mean within and between block dissimilarities.
Do you want the within block standard deviation of dissimilarities and
the between block standard deviation of dissimilarities?

If so, you could just grab the sources for meandist and change this
line:

out[take] <- tapply(dist, cl, mean)

to be

out[take] <- tapply(dist, cl, sd)

(or use `var` in place of `sd` if you want the variance instead of the
standard deviation.). Here is a function that does just that, using
`sd`:

sddist <- function (dist, grouping, ...) 
{
    mergenames <- function(X, Y, ...) {
        xy <- cbind(X, Y)
        xy <- apply(xy, 1, sort)
        apply(xy, 2, paste, collapse = " ")
    }
    grouping <- factor(grouping, exclude = NULL)
    cl <- outer(grouping, grouping, mergenames)
    cl <- cl[lower.tri(cl)]
    n <- table(grouping)
    take <- matrix(TRUE, nlevels(grouping), nlevels(grouping))
    diag(take) <- n > 1
    take[upper.tri(take)] <- FALSE
    out <- matrix(NA, nlevels(grouping), nlevels(grouping))
    out[take] <- tapply(dist, cl, sd)
    out[upper.tri(out)] <- t(out)[upper.tri(out)]
    rownames(out) <- colnames(out) <- levels(grouping)
    class(out) <- c("meandist", "matrix")
    attr(out, "n") <- table(grouping)
    out
}

## meandist
require(vegan)
data(dune)
data(dune.env)
dune.md <- with(dune.env, meandist(vegdist(dune), Management))
dune.sd <- with(dune.env, sddist(vegdist(dune), Management))

HTH

G

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%