Hi folks,
I have phylogeny with absolute branch lengths in million years. How do I
get a distance matrix with values between 0 and 1?
Best,
Eugen
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Hi Eugen,
to compute a distance matrix from a phylogeny, you can use the
cophenetic.phylo function in {ape}.
You then have to rescale all distances in you matrix (which are expressed
in million years) by the total depth of the tree:
dist=cophenetic.phylo(tree)
dist2=dist/max(dist)
Best,
OK, I started going through the Ives et al. paper - thanks for that. Note that
my data is not brain size vs. body size, but brain size vs. social group size
(not a measure for which brain size is a subset).
For our particular dataset, I believe we were not able to find much in the way
of
Thanks Liam,
OK, I'm starting to understand this better. But I'm not sure what now to do.
Given that the mathematics are such that a PGLS gives significance in one
direction, but not in another, what is the most convincing way to show that the
two variables really ARE associated (at some level
Tristan,
Check out the package devtools, and before submitting to CRAN make sure you
read: cran.us.r-project.org/doc/manuals/R-exts.pdf
There are obviously people on here who know a million times more than me,
and not that I've gotten very far, but I'm trying to figure this out myself
at the
Tom Schoenemann asked me:
With respect to your crankiness, is this the paper by Hansen that you are
referring to?:
Bartoszek, K., Pienaar, J., Mostad, P., Andersson, S., Hansen, T. F.
(2012). A phylogenetic comparative method for studying multivariate
adaptation. Journal of
Tristan-
I found this to be the most important how-to reference, but I am a windows user.
http://robjhyndman.com/hyndsight/building-r-packages-for-windows/
For distributing on CRAN, making help files and examples is the most
critical step. package.skeleton() is helpful in setting up the
