Re: [R-sig-phylo] Pairwise tree distance matrix

. Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2119 Life Sciences Addition, One Shields Ave. Davis, CA 95616 530-752-8086 dfu...@ucdavis.edu On Sep 21, 2013, at 3:00 AM, r-sig-phylo-requ...@r-project.org wrote

[R-sig-phylo] phylogenetic multiple regression of plant growth

. ...or an entirely different way of running these regressions. Thanks! Dan. -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 ___ R-sig-phylo mailing

Re: [R-sig-phylo] Phylogenetic signal in MCMCglmm

a phylogenetic mixed model regression with co-estimation of lambda, i.e. a way that doesn't lead to an optimization error. Perhaps MCMCglmm offers that? Thanks in advance for any input you could provide as to MCMCglmm and phylogenetic signal! Cheers, Dan. -- Daniel Fulop, Ph.D. Postdoctoral

Re: [R-sig-phylo] Phylogenetic signal in MCMCglmm

(phylo)/(var(phylo)+var(all other random effects + residuals)) (probably not including measurment errors) Best wishes, Shinichi On 24/07/2014, at 10:51 am, Daniel Fulop dfulop@gmail.com mailto:dfulop@gmail.com wrote: Dear R-sig-phylo list, I'm following up on a, seemingly

Re: [R-sig-phylo] Replacement of Phybase - species tree from gene trees

Hi, Just a quick suggestion. You could install the archived version of phybase in order to look at the R code for your function(s) of interest and then reuse that code directly in your own R scripts (or put them in separate scripts and source them). You can also then further taylor those

Re: [R-sig-phylo] fit Discrecte function of Geiger package

Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 510-253-7462 dfu...@ucdavis.edu [[alternative HTML version deleted

[R-sig-phylo] Is it okay to model species as a fixed effect in an LMM while also accounting for phylogenetic covariance?

to both DIC (from MCMCglmm) and AIC (from an lmer model w/o phylogeny). Thanks in advance for your feedback!! Dan. -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 [[alternative HTML

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Thanks, Graham ...but I'm not the OP. I was just shooting off a quick lead without actually checking the specifics in case it was useful. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

Re: [R-sig-phylo] Phylogenetic regression with a trait homologous within lower taxonomic groups, but analogous between higher taxonomic levels

: Sun, 07 Jun 2015 19:13:42 -0700 From: Daniel Fulop dfulop@gmail.com To: David Labonte dl...@cam.ac.uk Hi David, You're correct that if you build phylogenies for each your 4 groups and then connect all 4 in a polytomy (i.e. with zero branch lengths) then you would get an appropriate tree

Re: [R-sig-phylo] A perfect storm: phylogenetic trees, random effects and zero-inflated binomial data

effect - The fact that data are zero-inflated (most introductions fail). Any suggestions for R packages that can handle a binomial response variable, phylogenetic trees, random effects and zero-inflation? Thanks in advance, Diederik -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Isn't at least some of this functionality in mvSLOUCH and/or geiger? ...it's definitely the case that mvSLOUCH can handle missing data at the tips, and I think fossil data can be incorporated in it and geiger as well. At least Slater 2013 has code for incorporating fossils in geiger or

Re: [R-sig-phylo] Standalone version of AWTY

What about using Tracer instead? It's well-maintained with quite recent versions. [[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

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

Sergio, You can fit a non-Gaussian phylo regression with MCMCglmm. HTH, Dan. On Jun 17, 2015, at 9:40 AM, Sergio Ferreira Cardoso sff.card...@campus.fct.unl.pt wrote: Hello all, I'm having a problem with a Multiple Regression PGLS analysis that I'm performing. The residuals are

[R-sig-phylo] clade-specific release and radiate model?

tools or about how to roll my own. Thanks! Dan. -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] clade-specific release and radiate model?

, Daniel Fulop dfulop@gmail.com mailto:dfulop@gmail.com wrote: Hi All, Do you know if there are any methods out there for fitting ecological release and release and radiate models that are clade-specific? That is, in which the change in mode (OU to BM) happens

Re: [R-sig-phylo] clade-specific release and radiate model?

be much appreciated, especially about how to implement these clade-specific models with current tools or about how to roll my own. Thanks! Dan. -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis

Re: [R-sig-phylo] clade-specific release and radiate model?

function. Hope this helps, Brian On Fri, May 29, 2015 at 2:02 AM, Daniel Fulop dfulop@gmail.com mailto:dfulop@gmail.com wrote: Hi All, Do you know if there are any methods out there for fitting ecological release and release and radiate

Re: [R-sig-phylo] Will phyloXML in R be useful?

Sounds like a good idea. Not sure if you’re reinventing the wheel or not. Sounds like something ROpenSci might support; see: https://github.com/ropensci/onboarding From: George Vega Yon Reply: George Vega Yon