[R-sig-phylo] Including intraspecific variation (SE) in geiger::fitContinousMCMC

that in a single function? Thank you very much in advance, Diogo -- Diogo B. Provete, PhD Assistant Professor Biodiversity Synthesis lab <http://diogoprovete.weebly.com/> Biosciences Institute | Federal University of Mato Grosso do Sul | Brazil Associate Editor: Ecology and Evolution | Evo

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 148, Issue 7

Hi Susana, yes, the function picante::evol.distinct calculates the ES metric used in Jetz's et al DR metric https://www.rdocumentation.org/packages/picante/versions/1.8.1/topics/evol.distinct Best, Diogo Em sáb., 30 de mai. de 2020 às 06:02, escreveu: > Send R-sig-phylo mailing list

[R-sig-phylo] Bootstrapping loadings of phylo.pca

Hi Everyone, I'm trying to obtain the 95% CI for the loadings of a phylogenetic pca in order to improve the interpretation of axes. I'm trying to implement this in boot package by modifying this code that uses prcomp:

Re: [R-sig-phylo] estimate ancestral state with OUwie models

As far as I know, only the package bayou has a function to estimate ancestral states using OU. Rphylopars also does it using OU with missing data. Best, Diogo -- Diogo B. Provete Assistant Professor Institute of Biosciences Federal University of Mato Grosso do Sul Campo Grande, Mato Grosso do

[R-sig-phylo] How to incorporate intraspecific variation in MCMCglmm

ype_arena * type_og_stimulus, random = ~Specie + : prior$G has the wrong number of structures Thank you in advance, Diogo -- *Diogo B. Provete, PhD.* FAPESP Post-doctoral fellow Department of Environmental Sciences Centre for Sciences and Technologies for Sustainability Federal University of Sã

[R-sig-phylo] quantile regression in PGLS

Dear list, I was wondering if I could adjust a generalized least square model to part of my phylogeny, similarly to it's done in quantile regression, ie., select a few clades in a phylogeny and adjust a pgls to it. I want with this explore non-stationarity of the relationship between two traits

Re: [R-sig-phylo] variation in rates over time

Dear List, taking advantage of the discussion, I'd like to ask if I could do these test of rate heterogeneity in brownie.lite or auteur with a polytomous tree. Apparantly, auteur only accepts a fully dichotomous tree. Is there any alternative? Thank you in advance, Diogo -- Atenciosamente,

[R-sig-phylo] Hypothesis testing with phylosor

I have a doubt with using the picante::phylosor.rnd for testing hypothesis about the phylogenetic dissimilarities between sites. This function gives the randomized matrices obtained with the null model chosen. But how can I do to explicitly test for a significant difference between the observed

[R-sig-phylo] Phylogenetic autocorrelation and decomposition of trait diversity

Dear List, I have 2 data sets: one phylogenetic distance matrix, composed of 28 species of anuran amphibians, and a trait matrix composed of species by categories of visceral pigmentation on the surface of 20 organs [categories may vary from 0 (total absence of pigmentation) to 3 (surface of a