Hello,
So what you're suggesting is that I do that and then
fit<-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method="ML", right?
Thanks.
Best regards,
Sérgio.
ᐧ
2015-04-13 18:42 GMT+01:00 Liam J. Revell <[email protected]
<mailto:[email protected]>>:
Hi all.
I just wanted to add that it should be straightforward to sample
edge lengths as if they arose under a specific process. For
instance, here on my blog I show how to sample branching times &
edge lengths as if they arose under a pure-birth (i.e., 'Yule')
process, given a particular input topology:
http://blog.phytools.org/2015/__04/sampling-edge-lengths-__under-yule-process.html
<http://blog.phytools.org/2015/04/sampling-edge-lengths-under-yule-process.html>.
For things like the phylogenetic (contrasts) regression, this may be
preferable to Grafen's edge lengths, which tend to make recent edge
lengths very short, giving very high weight to the associated
contrasts.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.__revell/
<http://faculty.umb.edu/liam.revell/>
email: [email protected] <mailto:[email protected]>
blog: http://blog.phytools.org
On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote:
Hello,
Thank you both for the help.
Emmanuel, so is there a way to see contrasts in R? Reading this
paper
- Garland, T., Harvey, P. H., & Ives, A. R. (1992). Procedures
for the
analysis of comparative data using phylogenetically independent
contrasts.
Systematic Biology, 41(1), 18-32. - I was aware of the
importance of
standardizing contrasts and of comparing Absolute value of
standard contrat
vs Standard deviation of contrast. I've learned to do this in
Mesquite but
I don't know if R alows this to be done. When I run the GLS I
ask R to
estimate the rho, so, a priori I never know the rho value.
Maybe I'm really really confused, but here is the reason why I
tthink
something isn't right with my analysis: I built a phylogenetic
tree in
Mesquite, and based on several works I used million years as
branch
lengths. It makes sense for me because I'll be using a fossil
on my
analysis. But I tested the tree before adding the extinct taxa,
so to make
sure everything was OK when the tree was ultrametric. I noticed
that, for
example, whatever the independent variable (X) was, the alpha
from OU was
extremely high (0.999182, for instance). It would always be
0.999. I
thought maybe I was using the wrong transformation... That's why
I ended up
trying to know if I needed to do something prior to
transforming and
analysing the tree.
Thank you very much.
Best regards,
Sérgio.
ᐧ
2015-04-13 17:17 GMT+01:00 Emmanuel Paradis
<[email protected] <mailto:[email protected]>>:
Hi Sérgio,
There is indeed generally a relationship between branch
length
transformations and correlation structures. You may check
that with the
function vcv2phylo, e.g.:
tr <- rcoal(20)
co <- corGrafen(1, phy = tr)
ts <- vcv2phylo(vcv(co))
all.equal(tr, ts)
[1] FALSE
all.equal(compute.brlen(tr), ts)
[1] TRUE
compute.brlen() transforms the branch lengths according to
Grafen's model
with parameter rho = 1 (by default). Some other
transformations of branch
lengths are available in package geiger.
Best,
Emmanuel
Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit :
Hi everyone,
I'm relatively new in phylogenetic comparative methods.
I'm a little
confused about branch length transformations. I'm using
a tree with
divergence time (My) as branch lengths. When I use
corPagel, corGrafen or
corMartins in R, the branch lengths, are the branch
lengths automatically
transformed? e.g.,
gr.mammals<-corGrafen(1,phylo,__fixed=F);
fit<-gls(FCL~logBodymass,__correlation=gr.mammals,data=__df,method="ML").
My question may sound a bit nonsense but I've seen in
some papers (e.g.,
Spoor,
F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M.
T., & Walker, A.
(2007). The primate semicircular canal system and
locomotion. *Proceedings
of the National Academy of Sciences*, *104*(26),
10808-10812.) the
indication that a PGLS was made without branch
transformation, but no
reference is made to the model (maybe it's corBrownian).
Thank you very much.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
--------------------
Best regards,
Sérgio Ferreira Cardoso
MSc. Paleontology candidate
Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa
Geociências - Universidade de Évora
Lisboa, Portugal
