--
the data which you are trying to fit).
Hope this is not too confusing.
Take care,
Marguerite Butler
On Oct 26, 2009, at 8:53 AM, Andrew Hipp wrote:
Dear Fabio,
In ouch v2 and up, the root state is not treated as a free parameter
and is not returned. One way to think about your question might
Hi Alejandro,
The info you want is given in the example script of the dataset bimac, which is
included for ouch. To see the help page:
require(ouch)
data(bimac)
?bimac
Then what you need is:
tree - with(bimac,ouchtree(node,ancestor,time/max(time),species))
plot(tree,node.names=TRUE)
The
Hi David, Liam and everyone,
Reflecting traits at boundaries or absorbing them is something that can be
done, but I guess I'd like to encourage everyone to think carefully about the
interpretation of such simulations. What are you trying to model and what does
it mean at the end? Doing these
,
absorbing boundaries don't seem like a good model to me. I have never been able
to think up a good biological mechanism for a reflecting boundary.
Sorry for the extra email from the incomplete thought.
M
On Mar 5, 2011, at 8:50 PM, Marguerite Butler wrote:
Hi David, Liam and everyone
different from BM expectation. Perhaps,
the threshold model might be of a lot of use here; I'm going to have
to look into that much more.
Thanks for you advice, all!
-Dave
On Sun, Mar 6, 2011 at 12:50 AM, Marguerite Butler mbut...@hawaii.edu wrote:
Hi David, Liam and everyone,
Reflecting
Hi Andrew,
Does this sidestep the degrees of
freedom problem discussed by Garland et al.? Can anybody point me to
references discussing the mechanics of this process and why this is an
appropriate thing to do?
Others on this list will disagree with me, but it's not a degrees of
On Apr 1, 2011, at 7:57 AM, Marguerite Butler wrote:
Hi Alberto and Ted, and others,
Maybe this is too late to jump into the discussion, but I wanted to add a few
comments regarding analysis of the evolution of size and shape. I agree with
Ted that there are a number of important
Dear Kaspar,
Are your traits the same? Basically, are the seven color patches on the same
individual all one trait, or are they seven traits? Do all species have the
seven color patches? Or are the number of color patches variable? (this could
also be a character).
I think before you attempt
Hi Nina and everyone,
One thing to consider is that not all zero data are the same. Zeros under a
model of continuous trait evolution with a gaussian process as assumed under
Brownian motion and OU processes would occasionally cross zero, maybe go
negative, etc. For example if you were
Dear Elena,
If I understand you correctly, you are trying to fit a unique regime to each
branch of the tree?
This is not advisable, as there are more branches than there are more branches
than there are terminal taxa (data points). So you are trying to fit many more
parameters than you have
Dear Pas,
I am wondering what the general aim of your study is?
I agree with Ted, that you should be careful about your assumptions and the
tools you are using. Ted's point that K is a descriptive statistic is an
important one. K describes the expected divergence among tip traits assuming a
Oops. Sorry the citation is Schluter, Price, Mooers, Ludwig 1997. Likelihood of
ancestor states in adaptive radiation. Evolution 51:1699-1711. This issue has
been known for a long time.
On Jul 30, 2013, at 6:51 AM, Marguerite Butler mbutler...@gmail.com wrote:
Hi Tom,
One thing to keep
.
Is that problem resolved in these functions?
Best,
Sandra.
2013/10/26 Marguerite Butler mbutler...@gmail.com
Dear Sandra,
You might also want to look at the papers that go along with slouch,
ouch,
and ouwie. Here are some pdfs, along with some tutorials.
On my Rcompstart, the ouch stuff
FAX: 808-956-4745
http://butlerlab.org
http://manoa.hawaii.edu/biology/people/marguerite-butler
http://www2.hawaii.edu/~mbutler
> On Jun 11, 2018, at 7:33 PM, Simone Blomberg wrote:
>
> This sounded wrong to me, as the OU process should be agnostic to the
> dataset: There are no
gt;
> >
> > --
> > William Gearty
> > PhD Candidate, Paleobiology
> > Department of Geological Sciences
> > Stanford School of Earth, Energy & Environmental Sciences
> > williamgearty.com <http://williamgearty.com/>
> >
> >
hz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Marguerite A. Butler
Professor
Department of Biology
2538 McCarthy Mall, Edmondson Hall 216
Honolulu, HI 96822
Office:
7803sdata=ogCaep2DN92bk6%2FZwOOcpmHaCPQwX7BzNgKo2UMcWtw%3Dreserved=0
> >
> >>
>
>
> [[alternative HTML version deleted]]
>
> _______
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>
is called.
>
> So you make it work by removing "dat$" in the call to corBrownian():
>
> cbm <- corBrownian(1, tree, form = ~Species)
>
> Best,
>
> Emmanuel
>
> - Le 17 Mai 21, à 6:22, Marguerite Butler mbutler...@gmail.com a
> écrit :
>
.
Thanks again for your kind replies,
Marguerite
On Sun, May 16, 2021 at 8:58 PM Emmanuel Paradis
wrote:
> - Le 17 Mai 21, à 13:41, Marguerite Butler a
> écrit :
>
> Thank you very much for the reply Emmanuel!
>
> OK, yes I just tried and Iʻm surprised that this
archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
________
Marguerite A. Butler
Professor
Department of Biology
2538 McCarthy Mall, Edmondson Hall 216
Honolulu, HI 96822
Office: 808-956-4713
Dept: 808-956-8617
Lab: 808
lculate correlation separately
gls(Y ~ X, dat, correlation = cbm) ## works!
Thanks,
Marguerite
On Fri, May 14, 2021 at 10:21 PM Marguerite Butler
wrote:
> Aloha Oliver,
>
> From the cor.Brownian help page, the explanation for the form argument is
> this:
>
> a one si
at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http:/
Biology
2538 McCarthy Mall, Edmondson Hall 216
Honolulu, HI 96822
Office: 808-956-4713
Dept: 808-956-8617
Lab: 808-956-5867
FAX: 808-956-4745
http://butlerlab.org
http://manoa.hawaii.edu/biology/people/marguerite-butler
http://www2.hawaii.edu/~mbutler
[[alternative HTML version deleted]]
partment of Biology
2538 McCarthy Mall, Edmondson Hall 216
Honolulu, HI 96822
Office: 808-956-4713
Dept: 808-956-8617
Lab: 808-956-5867
FAX: 808-956-4745
http://butlerlab.org
http://manoa.hawaii.edu/biology/people/marguerite-butler
http://www2.hawaii.edu/~mbutler
[[alternative HTML version
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
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--
Marguerite
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