Hi Nathan,
Although it is still possible to impute the missing data prior to the analysis,
you can fit multivariate models with missing cases (NA values), using the
mvMORPH (development version) from my gitHubhttps://github.com/JClavel/mvMORPH/
Non-ultrametric trees (trees with fossil species) ar
Hi Diego,
This error occurs when traitDependentBAMM gets a posterior sample with no
rate shift, so that is why �the standard deviation is zero�.
Now we fixed this issue in the github version of BAMMtools,
https://github.com/macroevolution/bammtools
By the way, the manuscript describing this is s
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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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 al
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 modified
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
substanti
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 10:
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 <
Hi all,
I am performing an multivariate analysis in ouch on a group of extant
species. I would ideally like to include information for fossil taxa in the
analysis, however, no single fossil taxon preserves all of the variables of
interest. However, I have performed univariate ancestral state
recon
Hi all,
I am using BAMM and BAMMtools for analyse effect of a continuous trait
on evolutionary rates. But I have a problem with traitDependentBAMM
function, there is a warning which is repeated a lot of times:
1: In cor(rank(x), rank(y)) : the standard deviation is zero
On the other hand in
Hi Anand.
Have you tried eliminating spaces & line breaks from your Newick string.
When I do that I am able to read the tree with read.newick with no problem.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.
Hi Sergio,
there you go http://blog.phytools.org/2011/04/new-function-phylpca.html
http://cran.r-project.org/web/packages/phytools/index.html
best wishes
2015-06-04 11:26 GMT+01:00 Sergio Ferreira Cardoso <
sff.card...@campus.fct.unl.pt>:
> Dear all,
>
> I'm wondering if there is a package in
Hello
Dne Čt 4. června 2015 11:26:10, Sergio Ferreira Cardoso napsal(a):
> Dear all,
>
> I'm wondering if there is a package in R with which I can run a
> phylogenetic PCA. Please, if you know something or if you you know another
> software useful to use this technique, let me know.
Function ppc
Dear all,
I'm wondering if there is a package in R with which I can run a
phylogenetic PCA. Please, if you know something or if you you know another
software useful to use this technique, let me know.
Thanks in advance.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Card
Hi all,
thank you for your suggestions! I will delve into the suggested packages
and may come back to you when the learning curve becomes too steep :-).
thanks again,
Diederik
On 6/3/2015 5:44 PM, Peter Smits wrote:
> The alternative to MCMCglmm would be to use stan or bugs for writing
> your o
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