Re: [R-sig-phylo] VCV based on admixture?
Hello Jon, If I understand your question correctly I think maybe work by Garamszegi et al in Journal of Evolutionary Biology looking at the effects of shared ancestry and hybridization in dog breeds could be of interest. The article title is The role of common ancestry and gene flow in the evolution of human-directed play behaviour in dogs (here: https://onlinelibrary.wiley.com/doi/full/10./jeb.13567 <https://onlinelibrary.wiley.com/doi/full/10./jeb.13567>). A student of mine used the same approach to look at the relationship between size, reproduction and lifespan in 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 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 Site: http://alejandrogonzalezvoyer.com <http://alejandrogonzalezvoyer.com/> > On 19 Mar 2024, at 11:36, Jon wrote: > > Hello all, > > I've become involved in a small student project looking at spatial > variation in a very, very young group. There's discordance between the > mtDNA and nDNA trees, and good estimates of admixture based on population > genetic studies, between the different lineages (both mt and n lineages). > > I'm modeling size differences between lineages and attempting to detect > clear shifts in both average body size and sexual dimorphism. I don't see > any reason *per se* that a covariance structure based on admixture rates > (rather than strictly from the tree) wouldn't work, and it would *seem*to > allow for a not-strictly-bifurcating population history I suspect is the > case here...but I can't find anyone who has done something similar! > > Am I blind and there's some obvious paper I'm missing where covariance > between lineages was determined from something like admixture rates, or is > it a silly idea and I should just use the tree as an "average" covariance > and call it a day? > > Thanks! > > --Jon > > -- > Jonathan S. Mitchell <http://jonsmitchell.com> > Assistant Professor > Coe College > > [[alternative HTML version deleted]] > > ___ > 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 deleted]] ___ 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/
[R-sig-phylo] Announcement SSB Standalone meeting
Hello, I thought it could be of interest to this list to know that the next SSB Standalone meeting will take place in Mexico City. We hope to see you there! Spanish follows message in English. ENGLISH The Society of Systematic Biologist (SSB) and the Institute of Biology of the Universidad Nacional Autónoma de México (UNAM) are pleased to invite you to participate in the 5th Standalone Meeting of the Society of Systematic Biologists, to be held at the main campus of UNAM, Ciudad Universitaria, in Mexico City, on January 14th and 15th, 2023. The SSB Standalone meeting is one of the best opportunities to hear about state of the art research and novel methods in phylogenetic systematics. This is one of the most relevant meetings in the field, and for the first time will be held in Latin America. Most of the activities will take place at the main campus of UNAM, which is a UNESCO World Heritage site. The opening reception will be held at the National Biodiversity Pavilion, a newly inaugurated, one-of-a-kind venue that combines public museum exhibits with state-of-the-art research in biodiversity. The closing ceremony will be held at the Palace of Medicine, at the Historic Center of Mexico City, which housed the School of Medicine in the XIX century, and represents one of the best examples of architecture from the colonial period. Contributions for the meeting will be in two categories, lightning talks and posters. During the meeting forums and keynote talks on cutting edge phylogenetics will be presented, and pre- and post-meeting workshops will be held. In order to participate in the SSB meeting you have to be a SSB member. There are a number of benefits in being a member of SBB. In addition to participating in meetings, membership grants access to the Society journal, Systematic Biology. Students can also apply for travel grants and other benefits. Yearly membership ends 12-31-2023. The SSB and the Instituto de Biología have made an outstanding effort to offer travel grants and other benefits for students and posdoctoral researchers. This will be noticeable in registration rates and subsequent fees. Contact e-mail ssb.2023...@gmail.com Meeting information in full https://www.ib.unam.mx/ib/ssb2023/ Meeting registration https://www.ib.unam.mx/ib/ssb2023/registration-and-abstracts SBB membership application form https://www.systbio.org/membership.html ESPAÑOL La Sociedad de Biólogos Sistemáticos (SSB) y el Instituto de Biología de la Universidad Nacional Autónoma de México (UNAM) tienen el gusto de invitarles al 5o encuentro Anual Independiente de la SSB, a celebrarse en la Ciudad Universitaria de la UNAM, Ciudad de México, los días 14 y 15 de enero del 2023. La reunión de la SSB es una excelente oportunidad para conocer de primera mano los descubrimientos y métodos más recientes en biología filogenética. Esta reunión es uno de los foros más relevantes sobre el tema, y esta será la primera vez que se lleve a cabo en Latinoamérica. La mayor parte de las actividades transcurrirán en el campus de la UNAM, que es considerado patrimonio de la humanidad por la UNESCO. La recepción se llevará a cabo en el recientemente inaugurado Pabellón Nacional de la Biodiversidad, el cual conjuga funciones de difusión e investigación y es único en su tipo en Latinoamérica. La clausura se llevará a cabo en el Palacio de la Escuela de Medicina, ubicado en el Centro Histórico de la Ciudad de México, y que es un majestuoso ejemplo de la arquitectura virreinal de la Nueva España. Las modalidades de trabajos contempladas para esta reunión incluyen pláticas relámpago y carteles. Durante la reunión se llevarán a cabo foros y conferencias sobre tópicos de avanzada en el área y también se realizarán talleres pre y post-reunión. La participación en la reunión está restringida a las personas con membresía vigente en la SSB, por lo que es necesario inscribirse a esta sociedad científica. La membresía brinda múltiples beneficios: ademas de la participación en reuniones también incluye el acceso a la revista Systematic Biology. Adicionalmente, para estudiantes también incluye la posibilidad de solicitar apoyo económico para asistir a los eventos organizador por la Sociedad. La membresía anual es vigente hasta el 31-12-2023. La SSB y el Instituto de Biología de la UNAM han realizado un esfuerzo significativo para proporcionar apoyos para estudiantes y personas que realizan investigaciones posdoctorales, lo que se ve reflejado en el monto de la cuota de inscripción y de otras actividades. Correo-e de contacto ssb.2023...@gmail.com Información completa sobre la reunión https://www.ib.unam.mx/ib/ssb2023/ Registro para la reunión https://www.ib.unam.mx/ib/ssb2023/registration-and-abstracts Formato para inscribirse en la SSB https://www.systbio.org/membership.html Beneficios de la membresía a la SSB https://www.systbio.org/membership.html Alejandro ___ Dr Alejandro
[R-sig-phylo] PGLS incorporating weights and estimate of effect size
Hello, Co-authors and I want to run PGLS analyses including weights based on the number of individuals from which the dependent variable is estimated, as an estimate of the confidence of the species mean value. We’ve run models in gls with the necessary control for phylogenetic non-independence as well as the weights for the different observations. However, using gls we cannot obtain an estimate of effect size for the linear model. Is it possible to include said weights in phylolm, or another package that allows to estimate an effect size for the linear models? Cheers Alejandro ___ 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 Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web Site: http://alejandrogonzalezvoyer.com <http://alejandrogonzalezvoyer.com/> [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] Question regarding PGLS in caper
Hello Oliver, I completely agree with Julien. I’d add however that when running a PGLS with different branch length transformations you are in fact comparing among different models of trait evolution, which make different assumptions about how traits change along the phylogeny. Thus, I would 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 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 Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web Site: http://alejandrogonzalezvoyer.com <http://alejandrogonzalezvoyer.com/> > El 19 oct 2021, a las 9:22, Julien Clavel escribió: > > Hi Oliver, > > Your model comparison tells you that the "lambda" is better than "kappa", and > hence that it should provides a better phylogenetic structure for the > corresponding regression test. > > Making a model comparison to choose the structure is probably best practice, > but it also depends on the practicability. If I would have to stuck with a > single model from these three one (kind of omnibus transform) I would > probably choose "lambda" then, because at one extreme it reduces to the > classical OLS (lambda=0) and intermediate values (strength of "phylogenetic > signal") correspond to using a mixed model with BM random effects. This is > easier to interpret and directly relate to the signal to noise ratio of > phylogenetic structure in your model residuals. > > Cheers, > > Julien > > > De : R-sig-phylo <mailto:r-sig-phylo-boun...@r-project.org>> de la part de Oliver Betz > mailto:oliver.b...@uni-tuebingen.de>> > Envoy� : mardi 19 octobre 2021 01:02 > � : r-sig-phylo@r-project.org <mailto:r-sig-phylo@r-project.org> > mailto:r-sig-phylo@r-project.org>> > Objet : [R-sig-phylo] Question regarding PGLS in caper > > > Dear all: > > I am applying the pgls function in caper to test for the relationship > between a dependent and an independent variable. Usually, the > regressions can be well interpreted when applying the lambda branch > lenghth transformation. However, in one case, the regression became > only significant when I applied the kappa transformation, but remained > non-significant when I applied the lambda transformation. Does this > automatically mean that I should choose the kappa transformation in > this case? Or should I still stick to the AICc values and always > choose the model with the lowest AICc and the highest model weight? In > the described case, AICc for the (non-significant) lambda model was > lowest, i.e. it was lower (-36.7) than the (significant) kappa model > (-32.8). > > This brings me to a more general question: when using pgls in caper, > should I always compare (via AICc) bewteen the three branch length > transformation models (lambda, kappa, delta), or would it be > sufficient to stick to lambda to get an idea of the phylognetic > non-indepedence of the residual errors of the regression model? > > Thank you for any suggestions, > > Oliver Betz > > University of T�bingen, Germany > Institute of Evolution and Ecology > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > <mailto:R-sig-phylo@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > <http://www.mail-archive.com/r-sig-phylo@r-project.org/> > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > <mailto:R-sig-phylo@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > <http://www.mail-archive.com/r-sig-phylo@r-project.org/> [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] Number of parameters in Simmap
Hello Adrià The number of parameters in the model is equal to the number of transitions that are estimated, or free to vary. For example, if you have 3 states: A, B, and C, the ARD model estimates 6 rates, from A to B and vice versa, from B to C and vice versa and from A to C and vice versa. For the example you give below, if I understood correctly that you only have two trait-states, then if you fix B->A to 0 then that transition is no longer free to vary (thus not estimated by the model) and you’d only have a single transition being estimated, A->B. Cheers Alejandro ___ 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 Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web Site: http://alejandrogonzalezvoyer.com <http://alejandrogonzalezvoyer.com/> > On 21 Apr 2021, at 5:57, Adrià Bellvert wrote: > > Dear all, > I have been working with simmaps with the usual models (ER, ARD and SYM) > and some of my own ones. > The problem that I have come to is that I have the model ER and my model > that is ER but with the transition state that goes from A -> B but couldn't > turn back from B -> A. ER has 1 single parameter, but how many parameters > has my model and why? I need this information in order to be able to > compare these models based on AIC and choose the one most supported by my > data. > > Thanks in advance for any help > Adrià > > -- > *Adrià Bellvert* > PhD student. > *Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.* > *University of Barcelona.* > > [[alternative HTML version deleted]] > > ___ > 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 deleted]] ___ 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/
[R-sig-phylo] Simulating traits with different rates of evolution
Hello, A student of mine is analyzing whether the rates of evolution of a continuous trait depend on the state of a discrete trait. He finds no support for a model with different rates of evolution. However, we would like to test how different the rates would have to be in order for the method to support a two-rate model. Thus I would like to know how we could simulate trait evolution for the continuous trait with rates differing depending on the state of the discreet trait. Any suggestions are greatly appreciated. Best wishes, Alejandro ___ 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...@iecologia.unam.mx Lab website: www.alejandrogonzalezvoyer.com [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] Making ultrametric trees
Hi, >> Note that vcv(nonultrametric_tree, cor=TRUE) is different from >> vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my >> previous question (which one is preferred?) > > It (mainly) depends whether you want to assume a "clock-like" evolution for > the traits you are studying. Assuming that Sinichi is working with contemporaneous species, the assumption of comparative analyses is that the time available for phenotypic evolution (the off diagonal element of the VCV matrix) is the same for all species. The rate of phenotypic evolution may of course differ among species, but I think that this is not the same as allowing the expected change in the traits to depend on the branch lengths of a non-ultrametric tree, as would be the case in vcv(nonultrametric_tree, cor=TRUE). In such a case, a model allowing for variation in rate of trait evolution in conjunction with an ultrametric tree would be more appropriate. Of course, as pointed out by Brian, estimating divergence times is no piece of cake and there may be uncertainty associated with that step of phylogeny estimation 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 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Lab website: www.alejandrogonzalezvoyer.com > El 31/10/2016, a las 1:30 p.m., Emmanuel Paradis <emmanuel.para...@ird.fr> > escribió: > > Le 30/10/2016 à 03:09, Shinichi Nakagawa a écrit : >> Dear Emmanuel and Alejandro >> >> Many thanks for your replies. >> >> Emmanuel, I understand what you said if I use vcv(nonultrametric_tree, >> cor=FALSE) in a phylogenetic comparative method (PCM). But if I use >> vcv(nonultrametric_tree, cor=TRUE), isn't this the same as assuming a >> ultrametric tree? I may be missing something here? > > No, this is not necessarily the same thing since the off-diagonal elements of > the matrices may be different depending on how branch lenghts are changed by > chronoMPL (or other procedures you might use to make the tree ultrametric). > >> Note that vcv(nonultrametric_tree, cor=TRUE) is different from >> vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my >> previous question (which one is preferred?) > > It (mainly) depends whether you want to assume a "clock-like" evolution for > the traits you are studying. > > Cheers, > > Emmanuel > >> Many thanks >> >> Shinichi >> >> On Sun, Oct 30, 2016 at 9:53 AM, Alejandro Gonzlaez Voyer >> <alejandro.gonza...@iecologia.unam.mx >> <mailto:alejandro.gonza...@iecologia.unam.mx>> wrote: >> >>Hi, >> >>I would venture in adding that with an additive tree the differences >>in evol rates among species are determined by the genes used to >>estimate the tree, given differences in substitution rates among >>genes. I do think its important to bear in mind. >> >>Cheers >> >>Alejandro >> >>Alejandro Gonzalez Voyer >>Instituto de Ecologia >>UNAM >> >> >> >> >>> On Oct 29, 2016, at 2:45 PM, Emmanuel Paradis >><emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> wrote: >>> >>> Sure they are different. I forgot to mention that. >>> >>> In comparative analyses, the expected quantity of trait change (= >>the variance in the VCV matrix) is given by the product of the rate >>of evolution of the trait with branch length. So using a >>non-ultrametric tree is a way to assume different rates of evolution >>for each branch. With an ultrametric tree, you somehow assume a >>"clock-like" trait evolution (i.e., the quantity of change from the >>root of the tree to the tips is the same). >>> >>> BTW, the first command you give below should be (misplaced right >>parenthesis): >>> >>> vcv(chronoMPL(nonultrametric_tree), cor = TRUE) >>> >>> Best, >>> >>> Emmanuel >>> >>>> Le 29/10/2016 à 13:12, Shinichi Nakagawa a écrit : >>>> Dear Emmanuel >>>> >>>> Many thanks for your swift reply. >>>> >>>> If we get a correlation matrix, via chronoMPL [i.e. >>>> vcv(chronoMPL(nonultrametric_tree,
Re: [R-sig-phylo] Testing for relationship between one categorical and one continuous variable in a phylogenetic framework.
Hello Sean, If the continuous variable is the “response” and the “independent” variable the discrete one, you can use PGLS, this would be akin to an ANOVA and you can do it accounting for phylogenetic non-independence. Is this what you were after? Cheers 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...@iecologia.unam.mx Web: www.alejandrogonzalezvoyer.com > El 08/04/2016, a las 15:56, Sean McKenzie <mcken...@gmail.com> escribió: > > Hello, I have a two traits, one categorical (binary) and one continuous, > and I want to test for a relationship between them accounting for > phylogenetic signal. I have found a plethora of sources for examining > relationships between multiple categorical traits and many others for > examining multiple continuous traits, but I have been hard pressed to find > a test for one categorical and one continuous trait. A random blog post I > stumbled across said I could use either standard phylogenetic independent > contrasts (e.g. pic in ape) or general estimating equations (e.g. > compar.gee in ape). Unfortunately the examples only used continuous data > and tested for significance with regressions through the origin (e.g. > lm(var1_pic ~ var2_pic - 1) or compar.gee(var1 ~ var2 - 1, phy = tree) ). > This seems wrong when one variable was categorical, no? > > So, are PICs and PGEEs really appropriate for a single categorical and a > single continuous variable? If so, what is the appropriate way to test for > significance? If not, or if there's a better way, how can I test this? > > Thanks! > > Sean > > [[alternative HTML version deleted]] > > ___ > 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 deleted]] ___ 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/
Re: [R-sig-phylo] Determining Order of Trait Evolution
Hello Gavin, You could have a look at the method for evolutionary contingency, which works only for binary traits (meaning you’d have to transform your continuous trait into a binary one). See Pagel and Meade 2006 (Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible-Jump Markov Chain Monte Carlo in Am Nat) for details on the method. Note that it will provide information on whether evolutionary transitions in trait state for one of the traits is contingent on the state of the second one. You can infer the probable history of transitions from the results. 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 Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web: www.alejandrogonzalezvoyer.com > El 04/04/2016, a las 13:37, Gavin McLean Leighton <gm...@cornell.edu> > escribió: > > Hi all, > > > I have 500 trees of 80 species downloaded from birdtree.org and am primarily > interested in two traits. I have used PGLS to determine the traits are > related but would ideally like to test if there is an order to trait > evolution. To complicate matters one trait (Trait A) is continuous while the > second (Trait B) is presence/absence. I was hoping someone could direct me to > methods (assuming they exist) that would allow me to determine the estimated > value of Trait A before a gain of Trait B evolves in a lineage. > > > Thank you, > > Gavin > > > Gavin Leighton > NSF Postdoctoral Fellow > Cornell University > Cornell Laboratory of Ornithology > 159 Sapsucker Woods Road > Ithaca, NY > http://www.gavinmleighton.com/ > > > [[alternative HTML version deleted]] > > ___ > 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 deleted]] ___ 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/
Re: [R-sig-phylo] test random drift only?
Hello Franz, I don’t come with a solution but rather a suggestion, you should look at this paper: Revell, Harmon and Collar 2008 Phylogenetic signal, evolutionary process and rate. Systematic Biology 57: 591-601 In brief the authors of that paper point out that comparative methods analyzing trait evolution provide information about patterns in the data, however there may be different evolutionary processes that can lead to highly similar patterns in the data, thus it is hard to conclude anything about evolutionary processes only from information about evolutionary patterns. Cheers 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...@iecologia.unam.mx Web: www.alejandrogonzalezvoyer.com > El 04/03/2016, a las 11:00, f.k...@mailbox.org escribió: > > Dear everyone, > > I want to test if a trait evolved by random drift only without selection. > My hypothesis regarding a specific trait - I don’t want to tell which if it > turns out to be a good idea ;-) - is, > that there is no selection acting on it and it is evolving by random > mutations only. Thus u can see phenotypic differences between the species > but without selection advantage or disadvantage for the species. > > So now I’m looking for models and R packages. > I first thought about diversitree. make.quasse with and without drift and > compare the models… > However, the problem is, that my data is a discrete multitrait and not > continuous. Thus I think brownian motion models are not the right thing to > look at? > > Then I thought about just testing for clustering in the tips and compare with > a random distribution of the trait… > But since its its a multitrait and the phylogeny is not super big, I think > this method is not good for discriminating the randomness… > > I really hope anyone can give me some advice which methods might be suitable. > Are there any at all? > It seems its not easy since the only thing I really found was brownian > motion... > > Cheers, > Franz > > > > Franz-Sebastian Krah > PhD student, Fungal Ecology and Evolution > Plant Biodiversity Research Group > Technische Universität München (TUM) > Mobile: 0170 5221189 > Personal Website <http://franzkrah.github.io/> and University Website > <http://www.biodiv.wzw.tum.de/index.php?id=18> > > > > > > > > > > [[alternative HTML version deleted]] > > ___ > 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 deleted]] ___ 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/
Re: [R-sig-phylo] Non-ultrametric tree PGLS
Hi Sergio, I would add to Ted’s reply that you are not only considering alternative statistical models but that the evolutionary assumptions from the models you are fitting also differ, and you need to keep this in mind when comparing models. Comparison of AICs or any other estimate of goodness of fit must also involve careful consideration of the assumptions of the models you are comparing. In your particular case, the tree with branch lengths set to equal values (all branch lengths = 1) implies different amount of time to evolve for each of your species (in other words the expected 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 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 El 14/05/2015, a las 10:39, Theodore Garland Jr theodore.garl...@ucr.edu escribió: Hi Sergio, I am not quite understanding the situation nor why you see a problem. if I understand correctly, you are considering these five (5) alternative models for some sort of simple or multiple regression: OLS = star phylogeny PGLS with real-time branch lengths (ultrametric) Pagel's lambda with real-time branch lengths (ultrametric) PGLS with all branch legnths equal to 1.0 Pagel's lambda with all branch lengths equal to 1.0 To help decide which model best fits your data, you can look at AIC or for some comparisons do a likelihood ratio test. My experience is that any of the transform models (Pagel's lambda, Grafen's rho, OU in various implementations, ACDC) can sometimes yield really bizarre results when you start with a non-ultrametric tree. You need to be careful and check the REML likelihood surface for multiple peaks, etc. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/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: Thursday, May 14, 2015 8:32 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Non-ultrametric tree PGLS 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 Lambda is superior than 1 (both with ML and REML estimation). I suppose this is a consequence of the tree being non ultrametric. Is there a solution for this problem or should I, in this case, just ran a GLS (Brownian Motion) to avoid the over estimation of the phylogenetic signal? 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 ᐧ [[alternative HTML version deleted]] ___ 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/ ___ 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 deleted]] ___ 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/
[R-sig-phylo] Reminder: Conference on Phylogenetic Comparative Methods in Seville
Dear Colleagues, We are pleased to inform you that the list of keynote speakers for the conference on �Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology� (11th-15th November 2014, Seville, Spain) is now complete. Accordingly, the following experts will give plenary talks: Thomas F. Hansen (University of Oslo, Norway) Anthony R. Ives (University of Wisconsin-Madison, USA) Em�lia Martins (Indiana University, USA) Charles L. Nunn (Duke University, USA) Emmanuel Paradis (Institut de Recherche pour le D�veloppement, France) Samantha Price (University of California, Davis, USA) Liam Revell (University of Massachusetts, USA) In general, the conference will focus on phylogenetic comparative methods that are now widely used in very diverse fields of evolutionary biology to make robust inferences from interspecific data and phylogenies. Currently, we witness a rapid flourishing of the phylogenetic toolbox allowing researchers to tackle diverse questions concerning the evolution of species and their traits. We aim at providing a diverse overview on the most recent developments by the most prominent experts of the comparative methodology, and also at attracting an audience from different fields of evolutionary biology to demonstrate how the phylogenetic comparative approach can be used to address an ample array of biological questions in different taxa. We still welcome contributions to the main program (oral presentation or poster) For more info on the scientific and social program as well as for the registration, please visithttp://www.mpcm-evolution.org/conference/ . Please, note that places are limited! We look forward to seeing you in Seville! the organising committee: L�szl� Zsolt Garamszegi (Estaci�n Biol�gica de Do�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 Superior de Investigaciones Cient�ficas (CSIC) Av Am�rico 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/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] Conference on Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology
Dear colleagues, Given the scope of the conference I thought this mailing list would be a very appropriate forum to announce it. We are pleased to announce the upcoming conference entitled Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology, which will take place in Seville (Spain) from the 11th-15th November 2014. Overview: Phylogenetic comparative methods are now widely used in very diverse fields of evolutionary biology to make robust inferences from interspecific data and phylogenies. Currently, we witness a rapid flourishing of the phylogenetic toolbox allowing researchers to tackle diverse questions concerning the evolution of species and their traits. The conference aims at providing a bouquet of overviews on the most recent developments by the most prominent experts of the comparative methodology, and also at attracting a wide range of contributions from different fields of evolutionary biology to demonstrate how the phylogenetic comparative approach can be used to address an ample array of biological questions in different taxa. The list of invited speakers: Joe Felsenstein - University of Washington, USA (to be confirmed) Robert P. Freckleton -University of Sheffield, UK Thomas F. Hansen - University of Oslo, Norway Charles L. Nunn - Duke University, USA Emmanuel Paradis - Institut de Recherche pour le Développement, France Liam Revell - University of Massachusetts, USA We welcome proposals for talks and posters on any aspect of the application of the phylogenetic comparative methodology that is relevant for making evolutionary inferences. The deadline for applications is the 1st of September. Beside the scientific program, we also organise social events to obtain a unique cultural experience from 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 Carles Vilà - Estación Biológica de Doñana-CSIC, Spain Juan Arroyo - University of Seville, Spain the organising committee __ 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 page: http://consevol.org/people.html Personal web-page: http://consevol.org/members/alejandro_combo.html [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] Substitute for functions on the laser package
Hi Mariana, If you want to test for time-varying rates of speciation in your phylogeny another suggestion would be to look at Hélène Morlon's studies (e.g. Morlon et al 2010 PLoS Biology and Morlon et al 2011 PNAS), she has code for R which allows you to test the fit of various models of diversification, including decreasing or increasing rates of speciation. Cheers Alejandro On 4, Sep 2013, at 7:29 AM, Eliot Miller wrote: Hi Mariana, To install from tar.gz: rtm.wustl.edu/writings/htrtargz.pdf See also Liam's functions ltt() in phytools. Cheers, Eliot On Tue, Sep 3, 2013 at 11:20 PM, Mariana Vasconcellos marian...@utexas.eduwrote: Thanks, Liam! But, unfortunately I don't know how to build from source. I downloaded Xcode and the laser_2.3.tar.gz. But, I have no idea of how to install from source. If someone could help with any advise, that would be great! Also, does anyone have another option to calculate decreasing speciation rate, increasing extinction rate or both using a different package? Thank you very much! -- Mariana Vasconcellos Ecology, Evolution Behavior Integrative Biology The University of Texas at Austin On Sep 3, 2013, at 10:05 PM, Liam J. Revell liam.rev...@umb.edu wrote: Hi Mariana. You can download old versions of laser from the CRAN archive ( http://cran.r-project.org/src/contrib/Archive/laser/); however you will have to build from source. This is easy if you have Xcode (for Mac OS) or a gcc compiler installed. If you do not, and cannot figure out how to install from source, then respond to the list I'm sure someone will help out post a package binary for you. - Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 9/3/2013 10:39 PM, Mariana Vasconcellos wrote: Dear all: I just performed a test of the gamma-statistic on my tree and I found that diversification is not constant in time. So, I would like to perform the function fitSPVAR, fitEXVAR and fitBOTHVAR using the laser package. But, I just saw that the laser package was removed from the CRAN repository. Could anyone tell me what other alternative package I could use to develop and test models of decreasing speciation rate, increasing extinction rate or both? Does MEDUSA do this sort of analyses? Thank you for your help! Mariana [[alternative HTML version deleted]] ___ 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 deleted]] ___ 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 deleted]] ___ 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/ __ 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/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] lambda meaning on several traits
Hola Adrián, Here is my grain of sand. The lambda parameter you estimate gives you an idea of the evolutionary co-variance between all the traits included in the model, its the same interpretation as for the single trait, but in the case of multiple traits it provides information on the evolutionary co-variance as lambda estimates the phylogenetic signal of the residuals of the regression. An important point to add is that it is the evolutionary co-variance given the model of evolution, in this case Brownian motion, which has its underlying assumptions. You can look at recent papers by Tomas Hansen on this issue. There is quite a bit of literature on the subject, I can venture to recommend a few papers and maybe others in the list can add more: Martins and Hansen 1997 Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist 149 Rholf 2006 A comment on phylogenetic correction. Evolution 60: 1509-1515 Revell 2010 Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution 1: 319-329 Revell et al 2008 Phylogenetic signal, evolutionary process and rate. Systematic Biology 57: 591-601 Freckleton et al 2002 Phylogenetic analysis and comparative data: a test and review of evidence American Naturalist 160: 712-726 Freckleton 2009 Seven deadly sins of comparative analysis. J Evol Biol 22: 1367-1375 Cheers Alejandro On 8, Aug 2013, at 2:33 PM, Adrián Arellano Davín wrote: Hi all, First of all, I am very much a newbie in phylogenetics, so the question I will ask may be a bit naïve. Here it is: I want to correlate some phenotypic traits of several species of animals. Let's say, body mass and brain size. To account for the non-independence of the points, I must use PGLS. One way to do this is searching a lambda parameter that maximises the likelihood of my tree under a Brownian Model of evolution. I think I can understand the meaning of having a lambda value for one phenotypic trait. And I think it makes sense because it gives you a rough idea of what kind of evolution is going on. But, what is the purpose of calculating a lambda for several traits at the same time? Does it make sense at all? Is it just a mathematical trick with no biological meaning? Thanks in advance Adri [[alternative HTML version deleted]] ___ 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/ __ 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/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] Running chronopl on a multiphylo object
Hello
I would like to use the ape function chronopl on a multiphylo object which
contains a subsample of phylogenies from a Bayesian analysis. I've set up a
loop which runs chronopl iteratively on the sample of trees from the multiphylo
object but I seem to be doing something wrong when trying to concatenate the
ultrametricized trees - output from chronopl - into a new multiphylo object and
write a nexus file to export for use in another program.
This is the loop:
trees-read.nexus(MYTREES.nex)
newmulti-list(0)
for(i in 1:500){
newphy-chronopl(trees[[i]], 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: alejandro.gonza...@ebd.csic.es
Group page: http://consevol.org/people.html
Personal web-page: http://consevol.org/members/alejandro_combo.html
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Re: [R-sig-phylo] trait correlations with PICs
-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/ __ 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 (Under construction): Personal page: http://consevol.org/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] Ancestral state estimates of continuous traits
Hello, I am using ape to obtain ancestral state estimates for continuous traits. Two options are available, either maximum likelihood or a GLS method. I am comparing the results of both methods and one difference between the two puzzles me, I hope someone can enlighten me. Under GLS the ancestral state estimate at the root has virtually identical values for the point estimate and 95% confidence intervals, here is one example: 100 1.7848301 1.78483005 1.7848301 (100 is the root node number, then the ancestral state estimate and 95% CIs, respectively). However, when I use maximum likelihood for the same ancestral sate estimate, with the same data and tree I get the following result for the root : 100 1.6570119 0.86612615 2.4478977 (numbers in the same order as above). Any ideas as to why GLS gives such narrow confidence intervals for the ancestral state estimate 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 Web site (Under construction): Personal page: http://consevol.org/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] MRM(), AICc, and other ways to compare effects
Hi Roland, There are two functions for Rob's method to combine phylogenetic and spatial signal, although both - as far as I can tell - are based on gls methods, one uses independent contrasts, and thus I'm not sure if it is set up in such a way to allow you to include factors in the model. However, the other method is not based on independent contrasts but rather incorporates both matrices (the phylogenetic variance-covariance matrix and the geographical distance matrix) in the analyses, much as in typical PGLS analysis, therefore this method should - again if I am not 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-site (Under Construction): Group page: http://consevol.org/index.html Personal web-page: http://consevol.org/members/alejandro.html On 18, Sep 2012, at 4:48 PM, Luke Matthews wrote: Hi Roland, I haven't used Rob's method myself, but it might not be set up for factors. The lnam function isn't set up for factors either, but you should be able to use binary (0/1) variables in either method. You can perform the equivalent of adding a factor by coding it into separate 0/1 variables for the presence or absence of each factor level, leaving out one factor level because that will be your 'base' level. Then you add all these binary codings for the levels to the model at once. You can compare to the model without the full set of binary codings for levels to assess the difference in likelihood between including the factor in the model or leaving it out. Basically this is just having you do some of the steps that the machine does itself when you use a factor in a linear model. Don't do any messing about with taking only some binary level codings in and out, as then you would not be using them as a factor. You should only do that if you have a specific apriori hypothesis about a specific factor level, for example, Durkheim's famous hypothesis about reduced suicide among Catholics. You are correct that in lnam the factor variables (recoded into binary variables for #levels-1) should be entered as x. The phylogeny and geography correlation matrices should both be entered as W2 matrices. You use a syntax such as W2=list(phy.mat , geo.mat). The W1 matrix runs a qualitatively different autocorrelation used in some spatial and network research that models the distribution of the y variable itself rather than residuals of y. It is the distribution of residuals that you want to model. Best Luke -Original Message- From: Roland Sookias [mailto:r.sook...@gmail.com] Sent: Tuesday, September 18, 2012 3:28 AM To: Luke Matthews Cc: Alejandro Gonzalez Voyer; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] MRM(), AICc, and other ways to compare effects Cheers Luke and Alejandro Yes, I've been trying to use Rob's method. However I can't see how it allows incorporation of the other variables (communism, religion) I want as they are categorical/factors. How would you go about including these? I am interested in trying the lnam function. However I can't quite follow from the documentation how to implement what I need. Would you put the factor variables communism and religion in as x and the phylogeny and geography matrices as W1 and W2? Cheers Roland On Wed, Sep 12, 2012 at 3:21 PM, Luke Matthews lmatth...@activatenetworks.net wrote: Hi Roland and Alejandro, That is good to hear that Rob has the code already for his method to toggle the various matrices in and out to then assess likelihoods. Roland, you can also do this with the 'lnam' function from 'sna' package. You can fit your models with any combination of autocorrelation matrices and regular independent variables. It might be methodologically interesting to see what using both Freckleton's code and the 'lnam' code by Carter Butts produce, as the authors I'm sure don't know each other or each other's work. It would be neat to get some sense of how these implementations compare given that surely there are differences in the implementations even though they are essentially trying to do the same thing. Best Luke -Original Message- From: Alejandro Gonzalez Voyer [mailto:alejandro.gonza...@ebd.csic.es] Sent: Wednesday, September 12, 2012 2:23 AM To: Roland Sookias Cc: Luke Matthews; r-sig-phylo@r-project.org Subject: 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
Re: [R-sig-phylo] Non-parametric alternative to phylogenetic ANOVA?
Hi Karin, I would suggest setting all branch lengths to a unit value and then using corPagel() in ape as the model of trait evolution. Using corPagel the value of lambda is estimated simultaneously with model fit, lambda is an estimate of the phylogenetic signal in your residuals and basically adjusts the covariance among species so that the residuals fit a brownian model (Freckleton et al 2002 and Revell 2010 provide much more detailed explanations of all this), so it should work well even with equal branch lengths for your tree. You could also do as you suggested and transform branch lengths as suggested by Grafen and then repeat the analyses using corPagel as test of how sensitive results are to different branch length transformations. Based on the help files in ape, I understand corGrafen transforms branch lengths first following Grafen's method and then uses 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 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.html Personal web-page: http://consevol.org/members/alejandro.html On 31, May 2012, at 9:46 AM, Karin Schneeberger wrote: Dear Liam, dear Alejandro Thank you so much for your answers, that was very helpful! Just (hopefully) one last question: As branch lengths are not known for the tree I am using, I calculated them as suggested by Grafen (branch lengths being the number of descending taxa minus 1). So, I would replace corBrownian by corGrafen, proceed as suggested by testing the residuals for normality and conduct post-hoc tests if they don't differ from normal distribution, right? Thank you so much for your help. Best regards, Karin Von: Liam J. Revell liam.rev...@umb.edu An: Karin Schneeberger k.schneeber...@yahoo.de CC: Alejandro Gonzalez alejandro.gonza...@ebd.csic.es; r-sig-phylo@r-project.org r-sig-phylo@r-project.org Gesendet: 17:09 Mittwoch, 30.Mai 2012 Betreff: Re: [R-sig-phylo] Non-parametric alternative to phylogenetic ANOVA? Hi Karin. GLS with x as a factor is a generalized ANOVA which assumes [in the case of gls(...,correlation=corBrownian)] that the residual error in the ANOVA model has evolved by Brownian evolution. If you read your data into data frame Z with row names as species names, for instance: Z-read.table(filename,header=T,row.names=1) tree-read.tree(treefile) and your column name for the factor is x the column name for the continuous response variable is y, then you should just be able to do: fit-gls(y~x,data=Z,correlation=corBrownian(1,tree)) You can then perform various posthoc analyses from the gls object that is produced. For instance summary(fit) anova(fit) residuals(fit) As pointed out by Alejandro, you should check for normality of the residuals in residuals(fit) - not the normality of y before analysis. summary(fit) will also give you parameter estimated (fitted means for each factor) and standard errors. These can be used to conduct posthoc comparison of means using t-tests in the standard way. I hope this helps. All the best, Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 5/30/2012 10:46 AM, Karin Schneeberger wrote: Hi Alejandro Thank you for the very quick answer. I tried PGLS before, but then was told that GLS is not suitable for multistate categorical variables that can not be ranked (otherwise I would treat them as continuous). Also, with GLS it's as far as I understood not possible to state statistically whether certain groups are greater than others. But I am new into this kind of analysis and am very happy for any help and explanation, as I might be totally wrong. Cheers, Karin Von: Alejandro Gonzalezalejandro.gonza...@ebd.csic.es CC: r-sig-phylo@r-project.orgr-sig-phylo@r-project.org Gesendet: 16:26 Mittwoch, 30.Mai 2012 Betreff: Re: [R-sig-phylo] Non-parametric alternative to phylogenetic ANOVA? Hi Karin, You could use a gls method and look at the distribution of your residuals. It is the residuals which must be normally distributed, which can be checked using diagnostic plots such as a histogram or qq-plot of the residuals of your model. Cheers Alejandro On 30, May 2012, at 4:12 PM, Karin Schneeberger wrote: Dear all I'm trying to compare one trait across three (unordered categorical) groups including 25 species (let's say for example basal metabolic rate of aquatic, terrestrial and aerial
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I can send our Matlab code. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 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 ___ 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 Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web site (Under construction): Personal page: http://consevol.org/members/alejandro.html Group page: http://consevol.org/index.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[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)
: Dear Tom, There is no reason to assume that the residuals from your two PGLS analyses will be independent of phylogeny, so if you are going to do this you should correlate the residuals phylogenetically (i.e. run them through PGLS). General problems with using residuals as data have been commented on in the literature by people like Freckleton, but I think that in the situation where each variable of interest is regressed on the same confounding variable it is valid to use residuals - because the correlation between the residuals is the same as the partial correlation between them. However, the simplest solution for this analysis would be to regress A on B and C in a single PGLS. Rob Barton On 12/03/2012 11:00, r-sig-phylo-requ...@r-project.org r-sig-phylo-requ...@r-project.org wrote: 3. partial correlation with gls residuals? (Tom Schoenemann) Hello, I was hoping to get some feedback on whether I'm doing something legitimate. Basically, I have 3 variables (say: A, B, and C) measured on 100 species, and I want to see whether A and B correlate with each other after controlling for C, and for phylogeny at the same time. Here is what I thought seems reasonable: 1) do a gls with variable A predicted by variable C, using a corPagel correlations structure derived from a phylogeny of these species to control for phylogenetic effects. The residuals from this are then extracted 2) do a gls with variable B predicted by variable C, using the same method, also extracting the residuals for this comparison 3) do a simple lm of the residuals from step 1 vs. the residuals from step 2 I guess my question is, are the residuals from the gls independent of my phylogeny? If they are, then wouldn't this give me the partial correlation between A and B, controlling for C, and for phylogeny? Or is there a better (or alternative) way to do this? Thanks for any suggestions, -Tom - Professor Robert Barton Professor of Evolutionary Anthropology President, European Human Behaviour Evolution Association email: r.a.bar...@durham.ac.uk Address: Department of Anthropology, Durham University, Dawson Building, South Road, Durham, DH1 3LE U.K. Tel.+44 (0)191 334 1603 Mobile +44 (0)7507564773 RAI's 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/anthropology/research/earg/ Phylogeny of Sleep project: http://www.bu.edu/phylogeny/ Evolutionary Architecture of Reproduction project: http://www.dur.ac.uk/reproductionproject/ European Human Behaviour Evolution Association: http://www.ehbea.com/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/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 for the effects of a variable has been criticized, I include one paper on the issue by Rob Freckleton. 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 Construction): Group page: http://consevol.org/index.html Personal web-page: http://consevol.org/members/alejandro.html _ P. Thomas Schoenemann Associate Professor Department of Anthropology Indiana University Bloomington, IN 47405 Phone: 812-855-8800 E-mail: t...@indiana.edu Open Research Scan Archive (ORSA) Co-Director Consulting Scholar Museum of Archaeology and Anthropology University of Pennsylvania Homepage: http://mypage.iu.edu/~toms/ [[alternative HTML version deleted]] ___ 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 Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web site (Under construction): Personal page: http://consevol.org/members/alejandro.html Group page: http://consevol.org/index.html For PDF copies of papers see: http://csic.academia.edu
[R-sig-phylo] Estimating branch lengths on a fixed topology from molecular data
Hello, I was wondering if it is possible to estimate branch lengths on a fixed topology from a matrix of nuclear or mitochondrial DNA data. I used to do this in PAUP and would very much like to have an alternative in R. In PAUP one loaded a matrix of molecular data and a topology (without 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 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.html Personal web-page: http://consevol.org/members/alejandro.html [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Running fitDiscrete using try and if
Hi, I am trying to run simulations of evolution of discrete traits using fitDiscrete() in the package geiger. When the simulated data have very few changes in character state (or none) I get an error message: Error in fitDiscrete(phy, fcare[, i], model = ER, data.names = row.names(fcare), : ERROR: No solution found. Does your tree contain zero-length tip branches? The tree has no zero-length branches and it works fine with simulated data under somewhat higher rates of change using the same phylogeny. My problem is that I would like to use a loop to run several simulated data sets. But the loop stops whenever fitDiscrete() finds itself with one of the problematic datasets involving very low or no changes in character state and there seems to be no way of extracting the parameter values of previous runs of the loop. I was wondering it there was a way of creating a loop using try and if to avoid the loop crashing when the function tries to estimate rate of transition for data simulated under low rates of change. In such cases I would like it to simply skip to the next column of simulated data in the loop. 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 Web page: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] fitContinuous in geiger
into account certain decimals, and that might be the reason for these different results. Would anyone have any idea about why this happens and how I can deal with it in an informative way? Thanks so much for any help that you might be able to offer, Annemarie Verkerk ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/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 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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[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: alejandro.gonza...@ebd.csic.es Web-site: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg [[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] How to detect phylogenetic signal (lambda) in one unscaled trait?
Hi Alberto, The results differ between the two approaches because you're actually estimating two different things. gls(logY ~ logX, correlation=corPagel(1, tree), method=ML) Will give you the estimate of lambda for the residuals of the fitted model. while: fitContinuous(tree, log(Y/X), model=lambda) will give you the lambda value of the ratio of the two traits. Cheers, Alejandro On 23, Mar 2011, at 12:47 AM, Alberto Gallano wrote: Thanks Ted and Joe, that helps a lot with my understanding. Given then that the variables should be on a log scale, as you suggest, is there any reason to chose a regression model estimate of lambda: gls(logY ~ logX, correlation=corPagel(1, tree), method=ML) where X is a body size proxy (i.e., scaling is done in the model), over a ratio approach?: fitContinuous(tree, log(Y/X), model=lambda) These seem to produce different results. Is there a preference for one other the other in a comparative methods context? Or is this just a question of whether one prefers to size 'correct' using ratios vs residuals? kind regards, Alberto On Wed, Mar 23, 2011 at 1:30 AM, Joe Felsenstein j...@gs.washington.eduwrote: Ted wrote: Following on that, various papers (I can't remember the references) have argued that imagining Brownian-like evolution of body size on a log scale seems reasonable. That is, it should be equally easy for an elephant's body size to evolve 10% as for a mouse's body size to evolve 10%, and to analyze that you want everybody on a log scale. Extending this, you would want to use log(Y/X) or log(Y/[X raised to some allometric slope]). It's just easier to put all variables onto their log scales, so you have log(X), log(Y), log(Z) and then the allometric stuff just corresponds to linear combinations there, which you already have machinery to do. The recommendation to use log scales is a very old one: I talk about it in my Theoretical Evolutionary Genetics free e-text. But is older than that. Falconer has a whole chapter on Scale in his 1960 Introduction of Quantitative Genetics. Sewall Wright has a discussion of it in Chapter 10 of his 1968 first volume of Evolution and the Genetics of Populations (see pages 227ff.). But it is older than those -- for Wright also says (p. 228): Galton, as long ago as 1879, noted that the logarithms of measurements of organisms may be more appropriate than the measurements themselves on the hypothesis that growth factors tend to contribute constant percentage increments rather than constant absolute ones. The old biometrical types of the 1930s and 1940s knew all about this (though taking logarithms was tedious). It is only the more recent researchers who don't know 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 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 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 [[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] understanding lambda for single trait y versus gls(y~x)
Hi Andrew, The lambda value estimated for your dependent variable and the lambda value you get from the gls analyses differ because the second is the lambda of the residuals of your model. The lambda value of the model (which is estimated when you fit the gls) is a measure of the covariance in the residuals that results from the shared ancestry of the taxa as described by your phylogeny. Liam Revell has a very nice article about this in Methods in Ecology and Evolution. Cheers Alejandro On 17, Mar 2011, at 8:51 PM, Andrew Barr wrote: Hi all, My understanding of lambda is that it is a scalar multiplier for the off-diagonal elements of the variance covariance matrix computed from your tree. When lambda = 1, then the trait is evolving according to Brownian motion, when lambda = 0 there is no phylogenetic signal in the data. When I do a PGLS using packages ape and nlme I get a single estimate of lambda for the following model. myCor-corPagel(value=1,phy=myTree,fixed=F) gls(y~x, data=myDF, corr=myCor). I thought this single lambda value represented the estimate of lambda for variable y on myTree, but it is a different value than what I get when I use estimate lambda for variable y using package geiger fitDiscrete(phy=myTree,data=myDF$y,treeTransform=lambda). Using figDiscrete I get a value very close to zero, whereas the lambda estimated from the gls is around .65 and is significantly different from zero. Have I made an error, or do I not understand how lambda is being calculated? Thanks! Andrew Barr PhD Student Dept. of Anthropology University of Texas Austin ___ 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 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 [[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] multi-state categorical predictor variables in PGLS
Hi Andrew, As I understand it, gls() is doing a multiple generalized LS regression with as many dummy variables as there are factor levels. Is this a correct characterization? I think you'd get one dummy variable less than factor levels in your characterization (at least in regards to the number of levels for which parameters are estimated), as the gls sets one of the levels as the point of comparison with all other levels. Thus you'd get n-1 dummy variables for which the parameters are estimated. Having such a low value of alpha the results of the phylogenetic gls should be similar (if not identical) to results not taking phylogeny into account, as this suggests you don't have phylogenetic signal in the residuals of your relationship. There is a good paper on this issue by Liam Revell in Methods in Ecology and Evolution. There is also a function in geiger which allows you to run phylogenetic ANOVAs, but if I am not mistaken, the p-value is estimated based on simulations assuming traits evolve via Brownian motion (is this correct?). I've also seen lambda values below 0 in ape, theoretically lambda is described as being bounded between 0 and 1, but it could take values outside the bounds. I would be interested in hearing the thoughts of others in the list regarding whether lambda values for the Phylogenetic gls should be forced to be bounded between 0 and 1. This would more closely follow what has been proposed 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.es Web-site: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg On 7, Mar 2011, at 5:52 PM, Andrew Barr wrote: Hi everyone, I am trying to piece together the current best-practices for phylogenetic ANOVA with multi-state predictors. In my dataset, my four-level factor is non-random with respect to phylogeny. That is, if I know which higher level clade an species belongs to, I can predict with pretty good success which factor level it will be in. My understanding is that this situation likely overinflates my degrees of freedom and makes traditional F-tests inappropriate. I came across this paper (Garland et al 1993. Phylogenetic Analysis of Covariance by Computer Simulation. Systematic Biology 42:265 -292.) where the authors empirically recalculate critical values for F-ratios using computer simulations, tree topology, and a model of character evolution. I also have found that I can use PGLS (with ape and nlme) and specify my model like this. gls(myVar~myFactor,corr=corPagel(val=1,phy=myTree,fixed=F),data=myDF) As I understand it, gls() is doing a multiple generalized LS regression with as many dummy variables as there are factor levels. Is this a correct characterization? Does this sidestep the degrees of freedom problem discussed by Garland et al.? Can anybody point me to references discussing the mechanics of this process and why this is an appropriate thing to do? Finally, I get a negative value for estimated lambda. Any ideas on what that means? Thanks to everyone for any advice/references/. Andrew Barr PhD Student University of Texas at Austin results from my model Generalized least squares fit by REML Model: LIWI ~ Hab Data: aggast AIC BIC logLik -65.61627 -56.28418 38.80814 Correlation Structure: corPagel Formula: ~1 Parameter estimate(s): lambda -0.1480891 Coefficients: Value Std.Error t-value p-value (Intercept) 1.4492742 0.01876415 77.23635 0. HabH-0.0224975 0.03149986 -0.71421 0.4798 HabL-0.0668761 0.03066232 -2.18105 0.0360 HabO-0.1630386 0.02567505 -6.35008 0. Correlation: (Intr) HabH HabL HabH -0.686 HabL -0.794 0.485 HabO -0.936 0.594 0.542 Standardized residuals: Min Q1 Med Q3 Max -2.17865325 -0.60297897 -0.09760938 0.41995284 2.91201671 Residual standard error: 0.06913702 Degrees of freedom: 39 total; 35 residual ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Problems with fitDiscrete
Hello, I am trying to estimate transition rate parameters for simulated data using fitDiscrete in geiger. The data was simulated on an ultrametric phylogeny using sim.char. I've set the q matrix based on estimated transition parameters from a binary trait, on the same phylogeny where I now aim to run the simulations. The q matrix was set initially as: list(rbind(c(-0.01, 0.01), c(0.01, -0.01))). But when trying to estimate transition values using fitDiscrete under an equal rates model and no tree transformation I get the following message: Error in fitDiscrete(phy, fcare, model = ER, treeTransform = none) : ERROR: No solution found. Does your tree contain zero-length tip branches? At this point the simulation stops. I have already ran simulations with success using the same phylogeny, although in the previous simulations the q matrix had higher 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 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 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Phylogenetic ANOVA
Hello, Some colleagues and I are running some phylogenetic ANOVAS using the geiger package. In some of the analyses we get the same phylogentic p-value (very small p-value) even though the F-statistic differs between the two analyses, albeit it being relatively high in both instances. We were wondering why this arises, to get better grip on how the analysis works. We thought it may have to do with the randomizations to calculate the phylogenetic p-value. Or that the F-statistics are quite high... Below are two examples : m11-phy.anova(tree1,tmax,biozone,data.names=X,nsim=1000) Standard ANOVA: Analysis of Variance Table Response: td$data Df Sum Sq Mean Sq F valuePr(F) group 1 967.96 967.96 155.88 3.057e-12 *** Residuals 25 155.246.21 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Phylogenetic p-value: 0.000999001 m12-phy.anova(tree1,wt,biozone,data.names=X,nsim=1000) Standard ANOVA: Analysis of Variance Table Response: td$data Df Sum Sq Mean Sq F valuePr(F) group 1 602.88 602.88 109.01 1.333e-10 *** Residuals 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 ADDRESS NEW E-MAIL Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain E-mail: alejandro.gonza...@ebd.csic.es Tel: +34- 954 466700, ext 1749 Website (From my previous position): http://www.iee.uu.se/zooekol/default.php?type=personalpagelang=enid=146 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Estimating parameters of OU model using OUCH
Hello, I am interested in using the package OUCH to estimate parameters of an OU model of evolution for a suite of traits. I've been able to run the fitContinuous function in geiger without problems, but have hit an obstacle when it comes to OUCH. I think it probably has to do with how 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) Avenida Américo Vespucio s/n 41092 Sevilla Spain E-mail: alejandro.gonza...@ebd.csic.es Tel: +34- 954 466700, ext 1749 Website (From my previous position): http://www.iee.uu.se/zooekol/default.php?type=personalpagelang=enid=146 [[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] 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-project.org Subject: Re: [R-sig-phylo] Error message in gls analyses Le 06.11.2008 18:31, Alejandro Gonzalez Voyer a écrit : Hello, I am getting an error message when I run a gls analysis with APE. The message I get is: Error in glsEstimate(object, control = control) : computed gls fit is singular, rank 26 Could this be a result of multicolinearity problems or could it be because I have a model with too many 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. It's not clear what's wrong in this analysis, but my guess is that is that you don't have enough degrees of freedom in your model. Did you try with a simple model? EP Thank you, Alejandro Alejandro Gonzalez Voyer Post-doc. Animal Ecology, Department of Ecology and Evolution Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D 75236 Uppsala Sweden e-mail: alejandro.gonzalezvoyer[AT]ebc.uu.se Tel: ++46-18-471-2930 Web page: http://www.iee.uu.se/zooekol/default.php?type=personalpage http://www.iee.uu.se/zooekol/default.php?type=personalpageid=146lang=en id=146lang=en [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[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: where one tests whether the absolute value of independent contrasts is correlated with the heights of the nodes at which they are generated. Is there a way of implementing this analysis in R? Thank you, Alejandro [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
