Hi Dave,
Thanks a lot. It was exactly this I was trying to do.
Thank you all for your advice.
Cheers,
Sérgio.
- Mensagem original -
> De: "David Bapst" <dwba...@gmail.com>
> Para: "Sergio Ferreira Cardoso" <sergio.ferreira-card...@umontpellier.fr>
&
?
Thank you all, once again.
> De: "Eliot Miller" <et...@cornell.edu>
> Para: "Christoph Heibl" <christoph.he...@gmx.net>
> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
> <r-sig-phylo@r-project.org>, "Sergio
Hello all,
I'm using the package 'phytools' to try to add terminal branches to a tree
(attached). I tried to use add.everywhere function to add terminal branches. I
have 167 terminal taxa inside each of the 7 genera on my tree. Basically, I
just wanted to add some dozens of specimens to the
ds,
Sérgio.
- Mensagem original -
> De: "Emmanuel Paradis" <emmanuel.para...@ird.fr>
> Para: "Sergio Ferreira Cardoso" <sff.card...@campus.fct.unl.pt>,
> "r-sig-phylo" <r-sig-phylo@r-project.org>
> Enviadas: Terça-feira, 24 De Janei
Dear all,
I tried to estimate a value for alpha parameter of corMartins
(Ornstein-Uhlenbeck) but the output is a bit puzzling. I do as follows:
>
accessed from R
with the rotl package
(https://cran.r-project.org/web/packages/rotl/index.html)
Cheers,
-- François
On Fri, Jan 13, 2017 at 7:04 AM, Sergio Ferreira Cardoso
<sff.card...@campus.fct.unl.pt> wrote:
> Hello all,
>
> Do you know of any database where one can obtain a
Hello all,
Do you know of any database where one can obtain a good phylogeny of the
Amniota (in NEXUS or NEWICK file)?
Thank you.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
Best regards,
Sérgio Ferreira Cardoso
MSc. Paleontology
Dear all,
I was trying to find the pylogenetic signal for a trait and I used
phylosig():
phylosig(tree, trait, method="lambda", test=TRUE, nsim=999)
If I use, for instance, a lambda correlation in a gls, am I expected to
obtain the same value?
gls(trait~var1+var2,
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/liam.revell/
>> email: liam.rev...@umb.edu
>> blog: http://blog.phytools.org
>>
>> On 5/23/2016 12:11 PM, Sergio Ferreira Cardoso wrote:
>>
>>> Dear all,
>>>
>>&
Dear all,
I'm analysing a small data set consisting of values for 27 taxa. I am
extracting phylogenetic residuals from a regression (as in Revell, 2009) to
be used as size corrected values. Almost all the residuals are negative
because the regression line is positioned above what I would expect.
Dear members,
Does anyone know a way to make anova SS II with gls class objects? I've
tried Anova() from car package but it does not work with gls().
Thanks in advance.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
Best regards,
Sérgio
Hello members,
I'm creating relative values os semicircular canal size by fitting a PGLS
and extracting residuals (using phyl.resid). I've heard that R-squared
isn't meaningful in gls models. What I'm trying to do is to know is which
of the two independent variables is best and on a lm () model I
as
close species diverging into distinct niches and/or phenotypes.
Best,
Emmanuel
Le 16/07/2015 20:34, Sergio Ferreira Cardoso a écrit :
Hello all,
I'm trying to estimate a lambda for my phylogeny but something strange
happened. I used 3 different packages to confirm the estimated lambda
that it cannot be compared directly with values from OLS models.
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, July 20, 2015 4:11 AM
To: R phylo mailing list mailing list
Subject: [R-sig
Hello all,
I'm trying to estimate a lambda for my phylogeny but something strange
happened. I used 3 different packages to confirm the estimated lambda
value. My tree is ultrametric (with branchlengths in million years), it has
59 tips and 58 internal nodes. Here is what I did:
Thank you all for the suggestions. Creating a vector with the species works
very well. :)
2015-07-15 17:59 GMT+01:00 Sergio Ferreira Cardoso
sff.card...@campus.fct.unl.pt:
Thank you very much Nicholas. Works perfectly!!! :)
2015-07-15 17:22 GMT+01:00 Nicholas Crouch ncro...@uic.edu:
Sergio
Dear all,
I have a nexus file with 1000 trees on it with divergence times as branch
lengths. Does anyone know about a package that can make a consensus tree
out of my 1000 trees?
Thanks in advance.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
Ok. I just solved the problem with adding file= when using wirte.nexus.
2015-07-15 14:56 GMT+01:00 Sergio Ferreira Cardoso
sff.card...@campus.fct.unl.pt:
Thank you François,
I was trying to use consensus() from ape, but when I try to write a nexus
file I get an error message:
trees
,
Sérgio.
ᐧ
2015-07-15 14:49 GMT+01:00 François Michonneau
francois.michonn...@gmail.com:
Hi Sergio,
Not in R, but you can use PAUP, MrBayes or Dendropy (my recommendation).
Cheers,
-- François
2015-07-15 7:53 GMT-04:00 Sergio Ferreira Cardoso
sff.card...@campus.fct.unl.pt:
Dear
Dear members,
I have a tree with almost 10.000 species and I want to prune it. The
problem is I only want a tree with 59 of those species. Is there any
possible way to make this in R? Is there any code to prune all taxa except
the ones on my data?
Thanks in advance.
Best regards,
Sérgio.
--
Dear all,
When I try to get a list os phylogenetic residuals using phyres function
from R package I get this message: Error: could not find function phyres.
Does anyone know how to solve this problem?
phyres(fit.gls1)
Error: could not find function phyres
Best regards,
Sérgio.
--
Com os
Thank you both.
Best regards,
Sérgio.
No dia 24 de Jun de 2015 18:30, Theodore Garland Jr
theodore.garl...@ucr.edu escreveu:
Thank you, Liam!
Cheers,
Ted
From: Liam J. Revell [liam.rev...@umb.edu]
Sent: Wednesday, June 24, 2015 10:24 AM
To: Theodore Garland Jr; Sergio Ferreira Cardoso
/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/18/2015 6:16 AM, Sergio Ferreira Cardoso wrote:
Hello again,
Thanks for your help. This kind of solved my problem. I normally use
some kind of test (shapiro or komolgorov) to test for normality. I know
histograms or qqnorm plots
://blog.phytools.org
On 6/17/2015 12:40 PM, Sergio Ferreira Cardoso wrote:
Hello all,
I'm having a problem with a Multiple Regression PGLS analysis that I'm
performing. The residuals are not normal and it's difficult to bring them
to normality. In these cases, are there any alternatives
Hello all,
I'm having a problem with a Multiple Regression PGLS analysis that I'm
performing. The residuals are not normal and it's difficult to bring them
to normality. In these cases, are there any alternatives to the linear
model? I know that for non-phylogenetic analyses other models exist,
Dear all,
I just read this paper: Revell, L. J. (2009). Size‐correction and principal
components for interspecific comparative studies. Evolution, 63(12),
3258-3268. There is no coding for R, but it says it can be made using APE.
From what I could understand this is as simples as:
On 6/15/2015 7:41 AM, Sergio Ferreira Cardoso wrote:
Dear all,
I just read this paper: Revell, L. J. (2009). Size‐correction and
principal
components for interspecific comparative studies. Evolution, 63(12),
3258-3268. There is no coding for R, but it says it can be made using APE.
From
/phytools/index.html
best wishes
2015-06-04 11:26 GMT+01:00 Sergio Ferreira Cardoso
sff.card...@campus.fct.unl.pt:
Dear all,
I'm wondering if there is a package in R with which I can run a
phylogenetic PCA. Please, if you know something or if you you know another
software useful to use
Dear all,
I'm wondering if there is a package in R with which I can run a
phylogenetic PCA. Please, if you know something or if you you know another
software useful to use this technique, let me know.
Thanks in advance.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira
Hello all,
This isn't a specific question about phylogenies. Whenever I plot
prediction intervals for a linear model or a PGLS I can see what
observations fall out of the prediction intervals. My question is: if the
residuals of whatever regression model I'm using are normally/aproximatelly
Please, ignore this e-mail. Sent by mistake. Senseless.
Regards,
Sérgio.
No dia 16 de Mai de 2015 16:10, Sergio Ferreira Cardoso
sff.card...@campus.fct.unl.pt escreveu:
Hello all,
This isn't a specific question about phylogenies. Whenever I plot
prediction intervals for a linear model
are motivated by ties
to a possible set of biological processes.
Cheers,
Ted
*From:* Alejandro Gonzalez Voyer [
alejandro.gonza...@iecologia.unam.mx]
*Sent:* Thursday, May 14, 2015 8:47 AM
*To:* Theodore Garland Jr
*Cc:* Sergio Ferreira Cardoso; R phylo mailing list mailing
Hello all,
I have an ultrametric phylogenetic tree with divergence times as branch
lengths. To see if there was a big difference between using these branch
lengths and equal (=1) branch lengths I set all lengths to 1 and ran a
PGLS. I ran with Lambda transformations and the estimation is that
Dear all,
I performed a PGLS with a tree with divergence times as branch lengths. I
used 1 dependent and 1 independent variable. When I estimate the Lambda (in
Pagel's method) I get the Maximum Likelihood Lambda ~0 and the Restricted
Maximum Likelihood Lambda 0.878054. This is really strange. I
...@umb.edu
blog: http://blog.phytools.org
On 4/18/2015 1:15 PM, Sergio Ferreira Cardoso wrote:
Dear all,
I'm performing PGLS's with an ultrametric phylogenetic tree (divergence
time as branchlengths). I tied Pagel's Lambda transformation, OU
transformation, regular GLS and OLS, to compare
Dear all,
I'm performing PGLS's with an ultrametric phylogenetic tree (divergence
time as branchlengths). I tied Pagel's Lambda transformation, OU
transformation, regular GLS and OLS, to compare results. There is one
problem: the residuals of my analyses are not normal. I tried to remove big
sister branches). If you see a big outlier in the residuals,
then this is a problem - I would not trust the results. How do the
residuals look from a regular OLS analysis?
Cheers,
Ted
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio
Ferreira Cardoso [sff.card
: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 4/13/2015 2:04 PM, Sergio Ferreira Cardoso wrote:
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
Than you all.
Best regards,
Sérgio.
ᐧ
2015-04-13 22:02 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr:
Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit :
Hello,
Thank you both for the help.
Emmanuel, so is there a way to see contrasts in R?
Yes! The function pic() has been
of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
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
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
Dear all,
I'm trying to perform a PGLS with arbitrary branch lengths (I used branch
lengths = 1). The tree is non-ultrametric. Here is a result with Pagel's
Lambda:
vf-diag(vcv(tree))
fit-gls(FCLrelative~LogBodymass,correlation=Pagel,data=DF,method=ML,weights=varFixed(-vf))
summary(fit)
Model:
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