(log(g)^2)/MY: it�s about the accumulation of variance with time, and variance
has units squared.
And please don�t apologize for the question. You only have it because we as a
field have been sloppy about not including units with our measurements in
papers (I�m guilty of this, too). So it�s gre
Dear Sim�n,
Typically people do this by �painting� regimes on the tree using the discrete
trait and then trying different OU models for the different regimes. For
example, does being in the island regime lead to a higher rate of evolution
(bigger sigma in the BMS model) than being in the mainla
In addition to the ideas so far, there is also corHMM.
https://rdrr.io/cran/corHMM/man/corHMM.html is the main help for this, but you
can also use corHMM::ancRECON, corHMM:rayDISC, and corHMM:corDISC.
corHMM::plotRECON can plot ancestral state reconstructions.
For tip uncertainty, you can do 0&
Isn’t that what houwie does (which is fairly recently published)?
https://doi.org/10.1093/evolut/qpad002
Note my conflict of interest as a coauthor.
Best,
Brian
_
Brian O’Meara
He/Him
Professor, Dept. of Ecology & Evolutionary Biology
University of Tenne
).
Best,
Brian
_
Brian O’Meara
He/Him
Professor, Dept. of Ecology & Evolutionary Biology
University of Tennessee, Knoxville
From: Rafael S Marcondes
Date: Friday, February 2, 2024 at 1:45 PM
To: O'Meara, Brian C
Cc: r-sig-phylo
Subject: Re: [R-sig-
Hi, Russell.
Across taxa/clades, sure: clads (Maliet et al., 2019,
https://doi.org/10.1038/s41559-019-0908-0) or MiSSE (Vasconcelos et al., 2022,
https://doi.org/10./evo.14517) can do this. They paint different
diversification rates on different parts of the tree without requiring a priori
It should be character for everything. My fear with factor is that it’s
converting “2”, “3”, “1” to 1, 2, 3 if those are the numbers for the factor
labels. In general, I find avoiding factors makes life much easier (with
exception of some of the plotting in ggplot2).
A good way to check format
Hi, Jovana.
Geiger’s parameters aren’t quite what you described.
SE=NA: estimate what measurement error is, not assume it’s zero. This is then a
free parameter, penalized appropriately in the AIC calculations.
SE=0 (or run geiger with defaults): force the assumption that measurement error
is z
Hi, Rafa.
One thing to look at is whether the models are effectively identical; if the 3
state is 2 AICc worse than the 2 state it could be that it’s just adding a
single extra parameter with no improvement (i.e, the likelihoods might be the
same). In some of our other software we now have code
versity of Tennessee, Knoxville
From: James Boyko
Date: Friday, November 15, 2024 at 7:37 AM
To: liam.rev...@umb.edu
Cc: O'Meara, Brian C , Rafael S Marcondes
, r-sig-phylo , Jeremy
Michael Beaulieu
Subject: Re: [R-sig-phylo] Model-averaging corHMM models?
Ya I agree with Liam’s assessmen
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