Re: [R-sig-phylo] PGLS transformations

2015-04-13 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] PGLS transformations

2015-04-13 Thread Sergio Ferreira Cardoso
() 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

[R-sig-phylo] Weird estimated Lambda values (PGLS)

2015-05-08 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Weird estimated Lambda values (PGLS)

2015-05-09 Thread Sergio Ferreira Cardoso
/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Friday, May 08, 2015 3:33 AM To: r-sig

[R-sig-phylo] Residuals vs prediction intervals

2015-05-16 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] Non-ultrametric tree PGLS

2015-05-14 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Non-ultrametric tree PGLS

2015-05-15 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] PGLS transformations

2015-04-12 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] PGLS - branch lengths 1

2015-04-12 Thread Sergio Ferreira Cardoso
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:

Re: [R-sig-phylo] Non normal PGLS results

2015-04-18 Thread Sergio Ferreira Cardoso
...@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

[R-sig-phylo] Non normal PGLS results

2015-04-18 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Non normal PGLS results

2015-04-18 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] PGLS transformations

2015-04-14 Thread Sergio Ferreira Cardoso
: 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

Re: [R-sig-phylo] PGLS transformations

2015-04-14 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Residuals vs prediction intervals

2015-05-16 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Phylogenetic PCA

2015-06-05 Thread Sergio Ferreira Cardoso
/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

[R-sig-phylo] Phylogenetic PCA

2015-06-04 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] phyres function R package caper

2015-06-24 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Non Parametric PGLS

2015-06-18 Thread 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

Re: [R-sig-phylo] phyres function R package caper

2015-06-24 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] Phylogenetic size-correction

2015-06-15 Thread Sergio Ferreira Cardoso
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:

Re: [R-sig-phylo] Phylogenetic size-correction

2015-06-15 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Non Parametric PGLS

2015-06-18 Thread Sergio Ferreira Cardoso
://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

[R-sig-phylo] Non Parametric PGLS

2015-06-17 Thread Sergio Ferreira Cardoso
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,

Re: [R-sig-phylo] Weird abline

2015-07-22 Thread Sergio Ferreira Cardoso
of the analysis... ᐧ 2015-07-22 15:07 GMT+01:00 Sergio Ferreira Cardoso sff.card...@campus.fct.unl.pt: 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

[R-sig-phylo] ANOVA type II with gls()

2015-07-21 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] Weird abline

2015-07-22 Thread Sergio Ferreira Cardoso
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.

Re: [R-sig-phylo] Prune very large tree

2015-07-15 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] Build consensus trees

2015-07-15 Thread Sergio Ferreira Cardoso
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.

[R-sig-phylo] Different Lambda estimations

2015-07-16 Thread Sergio Ferreira Cardoso
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:

[R-sig-phylo] R-squared alternative for gls

2015-07-20 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Different Lambda estimations

2015-07-20 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] R-squared alternative for gls

2015-07-20 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Build consensus trees

2015-07-15 Thread Sergio 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

Re: [R-sig-phylo] Build consensus trees

2015-07-15 Thread Sergio Ferreira Cardoso
, 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

[R-sig-phylo] Prune very large tree

2015-07-15 Thread Sergio Ferreira Cardoso
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. --

[R-sig-phylo] Error in trees[[i]] : subscript out of bounds

2016-05-23 Thread Sergio Ferreira Cardoso
Dear all, I am trying to open a .tre file with ape. I downloaded the tree from http://www.timetree.org/book#treefiles. It's a .tre (not .nex) file, but it's essentially a nexus. I tried to open it: > tr <- read.nexus(file="TimetreeOfLife2015.tre") Error in trees[[i]] : subscript out of bounds I

Re: [R-sig-phylo] Error in trees[[i]] : subscript out of bounds

2016-05-23 Thread Sergio Ferreira Cardoso
>> 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, >>> >>&

Re: [R-sig-phylo] ape - corMartins

2017-01-25 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] ape - corMartins

2017-01-20 Thread Sergio Ferreira Cardoso
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: >

[R-sig-phylo] Phylogenetic signal

2016-09-22 Thread Sergio Ferreira Cardoso
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,

Re: [R-sig-phylo] Amniote Phylogenetic Tree

2017-01-14 Thread Sergio Ferreira Cardoso
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

[R-sig-phylo] Amniote Phylogenetic Tree

2017-01-13 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Sergio Ferreira Cardoso
? 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

[R-sig-phylo] Add terminal branches to tree

2017-06-19 Thread Sergio Ferreira Cardoso
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

Re: [R-sig-phylo] Add terminal branches to tree

2017-06-27 Thread Sergio Ferreira Cardoso
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> &