Re: [R-sig-phylo] Phylogenetic varying slopes and intercepts model

[Brian O'Meara]

Also worth noting is that people often use taxonomic levels if they don't
have a tree. Trees are more available than might be expected (though still
far less available than they should be), so you can get a tree and use
phylogenetic comparative methods.

Sources of trees:

https://tree.opentreeoflife.org/
https://www.treebase.org/
https://phylo.cs.nmsu.edu/
http://datelife.org/ (though the datelife R package
 may be more useful, depending on
scale)
https://datadryad.org/

Plus people make individual trees available: large trees for birds, sharks
and rays, plants, etc. that may not be deposited into a formal repository
but are on a website, plus trees stored as supplemental info in papers. So
if you're using taxonomy as a predictor because there doesn't seem to be a
good tree, there might actually be one with a bit of digging.

Best,
Brian

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On Wed, Sep 11, 2019 at 1:33 AM Joe Felsenstein 
wrote:

> Oscar Inostraza --
>
> Is the variable  x also evolving on the tree?  If so you need to use
> standard phylogenetically-informed comparative methods to estimate the
> variances and covariances of changes in both characters.
>
> You may not be able to assume that  y   responds instantly to  x.
>
> J.F.
> 
> Joe Felsenstein, j...@gs.washington.edu
> Department of Genome Sciences, University of Washington, Box 355065,
> Seattle, WA. 98195-5065 USA
>
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>
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Re: [R-sig-phylo] Phylogenetic varying slopes and intercepts model

[Joe Felsenstein]

Oscar Inostraza --

Is the variable  x also evolving on the tree?  If so you need to use
standard phylogenetically-informed comparative methods to estimate the
variances and covariances of changes in both characters.

You may not be able to assume that  y   responds instantly to  x.

J.F.

Joe Felsenstein, j...@gs.washington.edu
Department of Genome Sciences, University of Washington, Box 355065,
Seattle, WA. 98195-5065 USA

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