In Mesquite, make sure you have the "Branches proportional to lengths" option
checked so that the tree you are looking at shows the real branch lengths it
has! this is NOT the default option in Mesquite!
Cheers,
Ted
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio
Ferreira Cardoso [sff.card...@campus.fct.unl.pt]
Sent: Monday, April 13, 2015 10:13 AM
To: Emmanuel Paradis
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] PGLS transformations
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 <emmanuel.para...@ird.fr>:
> 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
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