Re: [R-sig-phylo] VCV based on admixture?

n dogs (https://www.journals.uchicago.edu/doi/10.1086/722531). Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Investigador Titular B Coordinación de Docencia y Formación de Recursos Humanos Instituto de Ecología Laboratorio de Conducta Animal Instit

[R-sig-phylo] Announcement SSB Standalone meeting

https://www.systbio.org/membership.html Beneficios de la membresía a la SSB https://www.systbio.org/membership.html Alejandro ___ Dr Alejandro Gonzalez Voyer Investigador Titular B Coordinación de Docencia y Formación de Recursos Humanos Instituto

[R-sig-phylo] PGLS incorporating weights and estimate of effect size

___ Dr Alejandro Gonzalez Voyer Investigador Titular B Coordinación de Docencia y Formación de Recursos Humanos Instituto de Ecología Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional

Re: [R-sig-phylo] Question regarding PGLS in caper

add that if you do go down the route of comparing such models, you need to think carefully first whether the models actually make sense for the traits you are comparing. Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Investigador Titular B

Re: [R-sig-phylo] Number of parameters in Simmap

jandro ___ Dr Alejandro Gonzalez Voyer Investigador Titular B Coordinación de Docencia y Formación de Recursos Humanos Instituto de Ecología Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autón

[R-sig-phylo] Simulating traits with different rates of evolution

___ Dr Alejandro Gonzalez Voyer Newton Advanced Fellow Investigador Titular B Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza

Re: [R-sig-phylo] Making ultrametric trees

stimation as well. Cheers Alejandro _______ Dr Alejandro Gonzalez Voyer Newton Advanced Fellow Investigador Asociado C Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónoma de México México, D.F. 04510 México Tel: +52

Re: [R-sig-phylo] Testing for relationship between one categorical and one continuous variable in a phylogenetic framework.

___ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web

Re: [R-sig-phylo] Determining Order of Trait Evolution

. However, you should be careful as the method is sensitive to trait-state distribution. Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional

Re: [R-sig-phylo] test random drift only?

Alejandro ___ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza

Re: [R-sig-phylo] Accounting for phylogeny in binary predictor, binary response data

Hi, I received the very same E-mail, also disguised as a reply to my message. Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional

Re: [R-sig-phylo] Accounting for phylogeny in binary predictor, binary response data

you should take this into account - if it applies - when interpreting your results. Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónom

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

variances - diagonal terms in the variance-covariance matrix - differ between the species), and thus you should consider whether such an assumption makes biological sense in your system. Cheers Alejandro ___ Dr Alejandro Gonzalez Voyer Laboratorio

[R-sig-phylo] Reminder: Conference on Phylogenetic Comparative Methods in Seville

�ana-CSIC, Spain) Alejandro Gonzalez Voyer (Estaci�n Biol�gica de Do�ana-CSIC, Spain) Carles Vil� (Estaci�n Biol�gica de Do�ana-CSIC, Spain) Juan Arroyo (University of Seville, Spain) __ Alejandro Gonzalez Voyer Post-doc Estaci�n Biol�gica de Do�ana Consejo

[R-sig-phylo] Conference on Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology

Andalusia. For more info on the conference and how to apply please go to http://www.mpcm-evolution.org/conference/ We look forward to seeing you in Seville! László Zsolt Garamszegi - Estación Biológica de Doñana-CSIC, Spain Alejandro Gonzalez Voyer - Estación Biológica de Doñana-CSIC, Spain

Re: [R-sig-phylo] Mesquite issues

e archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@

Re: [R-sig-phylo] gls in package nlme

error: 8.118852 > Degrees of freedom: 103 total; 39 residual > > > Thank you for any suggestions. > cheers, > > Jorge S. Gutierrez > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archiv

Re: [R-sig-phylo] Substitute for functions on the laser package

R-sig-phylo mailing list - R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>>> >> >> >>[[alternative HTML version delet

Re: [R-sig-phylo] lambda meaning on several traits

phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: +

[R-sig-phylo] Running chronopl on a multiphylo object

]], lambda=0.5) newmulti<-c(newphy, newmulti)} Any help is welcome!! Cheers Alejandro ______ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 466700, ext 1749 E-mail: ale

Re: [R-sig-phylo] trait correlations with PICs

gt; Thanks a lot in advance and best wishes from Switzerland, > Anne > > > -- > Dr. Anne Kempel > Institute of Plant Sciences > Altenbergrain 21 > 3013 Bern > Switzerland > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman

Re: [R-sig-phylo] trait correlations with PICs

oject.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científi

[R-sig-phylo] Ancestral state estimates of continuous traits

basal node? Cheers Alejandro __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Hi Antigoni You can try ape (and nlme) with the functions gls and corPagel (the latter to define the covariance structure, ie the evolutionary model) and also caper (I don't know the exact function there). Cheers Alejandro _ Dr. Alejandro Gonzalez

Re: [R-sig-phylo] MRM(), AICc, and other ways to compare effects

t mistaken - allow you to include factors. Cheers, Alejandro __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web-s

Re: [R-sig-phylo] MRM(), AICc, and other ways to compare effects

Hi, Yes this is possible, look at Freckleton and Jetz 2009. Rob has R code for two functions allowing to combine geographic and phylogenetic matrices. Cheers Alejandro _ Dr. Alejandro Gonzalez Voyer Estación Biológica de Doñana (CSIC) Avenida Américo

Re: [R-sig-phylo] Comparative analyse and heritability

andro ______ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web-site (Under Construction): Group page: http://consevol.org/index

Re: [R-sig-phylo] Non-parametric alternative to phylogenetic ANOVA?

s the "traditional variance-covariance matrix for the phylogeny", which I understand to be a brownian model (ie corBrownian). Hope this helps. Cheers Alejandro ______ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Ves

Re: [R-sig-phylo] Non-parametric alternative to phylogenetic ANOVA?

s phylogeny that > also returns which groups differ from each other? > > Your sincerely, > Karin > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://st

Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)

; South Africa > > >[[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > _

Re: [R-sig-phylo] 3. partial correlation with gls residuals? (Tom Schoenemann)

First Annual Postgraduate Conference at Durham 2011: >> http://www.dur.ac.uk/rai.postgrad/ <http://www.dur.ac.uk/rai.postgrad/> >> >> >> Department: http://www.dur.ac.uk/anthropology/ >> Evolutionary Anthropology Research Group: >> http://www.dur.ac.uk/an

[R-sig-phylo] Estimating branch lengths on a fixed topology from molecular data

branch lengths) with identical species coverage, then branch lengths were estimated using maximum likelihood (could also use parsimony) and given settings for the substitution model. Any tips would be appreciated! Best wishes Alejandro __ Alejandro Gonzalez Voyer

[R-sig-phylo] ace of continuous traits

I've run analyses with several traits on exactly the same phylogeny and I see this for all traits. Cheers Alejandro __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 4

[R-sig-phylo] Running fitDiscrete using try and if

Alejandro __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web page: https://docs.google.com/View?id=dfs328dh_

Re: [R-sig-phylo] fitContinuous in geiger

kelihood >> [1] -2067.052 >> sd log-likelihood >> [1] 213.44 >> >> There are no no more lambda scores of ‘1’ in the data, but the log >> likelood is a really big number, and I'm not sure what that would mean >> in this context? >> >> So,

Re: [R-sig-phylo] How to detect phylogenetic signal (lambda) in one unscaled trait?

it. >> >> Joe >> ---- >> Joe Felsenstein j...@gs.washington.edu >> Department of Genome Sciences and Department of Biology, >> University of Washington, Box 355065, Seattle, WA 98195-5065 USA >> > > [[alternative HTML version deleted]] > > ___

[R-sig-phylo] R-sig-phylo list

Here is the Email: R phylo mailing list mailing list Cheers Alex __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es

Re: [R-sig-phylo] understanding lambda for single trait y versus gls(y~x)

> ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo __ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS Estación Biológica de Doñana Consejo Superior

Re: [R-sig-phylo] multi-state categorical predictor variables in PGLS

in the literature wouldn't it? Cheers Alejandro __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain Tel: +34- 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.e

[R-sig-phylo] Identifying nodes in ouch tree

nd to specific nodes on the phylogeny? Or do I simply have to make it out from the information available using print(ouchtree object)? Thanks, Alejandro ______ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas

[R-sig-phylo] Problems with fitDiscrete

r transition values. I've tried increasing the value of the q matrix (to 0.02) but I still get the same message. Any ideas as to what may be causing the problem? Thank you. All the best! Alejandro ______ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS Estaci

[R-sig-phylo] Question regarding simulate character option in geiger

and table with a trait called data: cp<-corMartins(2.5, tree, fixed=TRUE) C<-corMatrix(Initialize(cp, data)) sim.char(tree, model.matrix=C, nsims=100, model="brownian") Cheers, Alejandro ______ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS & NEW

[R-sig-phylo] Phylogenetic ANOVA

uals 25 138.265.53 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Phylogenetic p-value: 0.000999001 Cheers, Alejandro __ Alejandro Gonzalez Voyer Post-doc NEW ADD

[R-sig-phylo] Difference in alpha value estimates between geiger and OUCH - data

Hello,Sorry for not sending in any data to replicate the problem I posted in the list. I now include as attachment a small database and phylogenetic tree in Nexus format. Carl Boettiger pointed out correctly that the cases in which I found a large difference between alpha estimates probably also ha

[R-sig-phylo] Different estimates of alpha with geiger and OUCH

0.5 108.14 Cheers, Alejandro ______ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 4

[R-sig-phylo] Estimating parameters of OU model using OUCH

w the data need to be organized in OUCH. I would greatly appreciate any tips to run the hansen function in OUCH, especially regarding data organization. Cheers Alejandro ______ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS & NEW E-MAIL Estación Biológica de Doñ

[R-sig-phylo] Use of OUCH package

w the data need to be organized in OUCH. I would greatly appreciate any tips to run the hansen function in OUCH, especially regarding data organization. Cheers Alejandro ______ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS & NEW E-MAIL Estación Biológica de Doñ

Re: [R-sig-phylo] Error message in gls analyses

Thank you Emmanuel. I think it was indeed a problem with degrees of freedom, too many independent variables. Best wishes, Alejandro -Original Message- From: Emmanuel Paradis [mailto:[EMAIL PROTECTED] Sent: den 10 november 2008 09:09 To: Alejandro Gonzalez Voyer Cc: r-sig-phylo@r

[R-sig-phylo] Error message in gls analyses

independent variables for the number of clades included in the analysis? I have 26 clades and tried running the analysis with 7 independent variables and still get an error message. Thank you, Alejandro Alejandro Gonzalez Voyer Post-doc. Animal Ecology, Department of Ecology and

[R-sig-phylo] Detecting non-Brownian trait evolution

Hello, I want to analyze whether the evolution of certain traits within a clade fits a niche-filling model. I've looked at GEIGER and the different tests offered within that package to analyze the tempo and mode of evolution of continuous traits. I also wanted to implement the Node height test:

[R-sig-phylo] Beta coefficients in R

standard deviation of Y? I have looked for information on this in the R and APE help sections but was unsuccessful. Thank you! Best wishes, Alejandro Alejandro Gonzalez Voyer Post-doc. Animal Ecology, Department of Ecology and Evolution Evolutionary Biology Centre

[R-sig-phylo] GLS with APE questions

regression coefficients in the multiple regression model. This would be great as one could present to readers a measure of the contribution of each of the variables to the explanation of the variance in the dependent variable. Thanks, Alejandro Alejandro Gonzalez Voyer