Hi Ting-Wen,
here is a short function to do this (also available at
https://gist.github.com/skembel/7240466 ):
#prune tree to get rid of very closely related tips
otuPhylo <- function(phy, cutoff=0.05) {
dists <- cophenetic(phy)
diag(dists) <- NA
pruned <- vector()
for (i in
Hi all,
I would like to prune several taxa with short distances between each other from
a tree by setting a specific threshold and keep one of these taxa, but in the
end I got all these taxa out...
Following is a simple example I used, but ended in a wrong tree, not I expected.
# the original
Hi Krishna,
> (1) I'd like to examine the links between group size (cont. outcome) and
> various social network measures (cont. predictors) across 10 species of
> nonhuman primates. I first tried implementing the PGLS code in Caper
> package that incorporates random-sampling of intraspecific
