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] 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] Substitute for functions on the laser package

://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

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

/ __ 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 site: Personal page: http://consevol.org

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

(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: alejandro.gonza...@ebd.csic.es Group

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

://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

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

at the 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] MRM(), AICc, and other ways to compare effects

- 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-site (Under

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

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 Vespucio s/n 41092

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

___ 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 Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo

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

/mailman/listinfo/r-sig-phylo On Mar 12, 2012, at 6:10 AM, Alejandro Gonzalez V wrote: Hello, Why not simply use multiple regression ie A ~ B + C using gls and a correlation structure to control for phylogeny? Are you worried about multicolinearity? Use of residuals to control

[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] Running fitDiscrete using try and if

__ 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_14gwwqsxcg

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

/mailman/listinfo/r-sig-phylo ___ 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 Estación Biológica de Doñana Consejo

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

Here is the Email: R phylo mailing list mailing list r-sig-phylo@r-project.org 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

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

]] ___ 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 de

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

__ 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 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web page: https

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

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-site: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg

[R-sig-phylo] Problems with fitDiscrete

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 Estación Biológica de Doñana Consejo

[R-sig-phylo] Phylogenetic ANOVA

'***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Phylogenetic p-value: 0.000999001 Cheers, Alejandro __ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS NEW E-MAIL Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain E-mail

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

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 Doñana (CSIC

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] 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