findzeros <- function(d, both=F, names=T) {
# find the pairs of sites with 0 distance in a distance matrix
# input: distance object (e.g. from dist() or vegdist()
# output: matrix of pairs of sites with dist=0
#  default is only unique pairs, but both=T gives both
# return site names if names=T otherwise return indices

dm <- as.matrix(d)
rm <- row(dm)[dm==0]
cm <- col(dm)[dm==0]
# keep non-diagonals (both=T) or upper triangle (if both=F)
if (both) { keep <- rm != cm}
 else {keep <- rm < cm }		# ifelse() doesn't seem to work here

sites <- dimnames(dm)[[1]]
if (names) {cbind(row=sites[rm[keep]],col=sites[cm[keep]]) }
  else {cbind(row=rm[keep],col=cm[keep]) }
}