Hi Nathan,
A bit late answer due to vacation but you can also try to use my mvSLOUCH
package (on CRAN). While it (still) does not allow for explicit fossil species
you can a very short tip branch at the place where the fossil should be. For
missing observations you write NAs, the package has no
Hi Daniel,
There’s a difference between a method being able to handle fossil data, that is
a dataset consisting of a non-ultrametric tree an data for all tips including
non contemporaneous ones, and a method allowing you to directly specify trait
values at nodes. Most trait evolution methods
Oops - sorry Daniel, yes that should have been addressed to Nathan...
Graham Slater
Peter Buck Post-Doctoral Fellow
Department of Paleobiology
National Museum of Natural History
The Smithsonian Institution [NHB, MRC 121]
P.O. Box 37012
Thanks, Graham ...but I'm not the OP. I was just shooting off a quick
lead without actually checking the specifics in case it was useful.
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R-sig-phylo mailing list - R-sig-phylo@r-project.org
To: dfulop@gmail.com
Date: Thu, 4 Jun 2015 21:22:46 +
CC: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] Constraining node values in an OUCH analysis
Hi Daniel,
There�s a difference between a method being able to handle fossil data, that
is a dataset consisting of a non-ultrametric
Couldn't remember, so went and looked. Turns out that NAs are a problem in
the tips. This isn't necessitated by the structure of the problem, only by
the structure of the package, i.e., because ouchtrees are constructed in
ignorance of where the data are. Unfortunately, it will require
Aaron,
While contemplating Nate's question, I wondered, doesn't hansen
currently support NA codings for missing variables for tip taxa?
Unfortunately the donotrun{} example for hansen() using geiger data
isn't currently functioning, so I couldn't test this.
-Dave Bapst
On Thu, Jun 4, 2015 at
Interesting question, Nate. Do I understand you to say that you have data
on some variables (and not others) at internal nodes? If so, what happens
when you just add those to the data, with NA to indicate missing values?
Have you tried this?
A.
On Thu, Jun 4, 2015 at 11:10 AM, Nathan Thompson
Isn't at least some of this functionality in mvSLOUCH and/or geiger?
...it's definitely the case that mvSLOUCH can handle missing data at the
tips, and I think fossil data can be incorporated in it and geiger as
well. At least Slater 2013 has code for incorporating fossils in geiger
or
