[R-sig-phylo] Including intraspecific variation (SE) in geiger::fitContinousMCMC
Dear list, we have a dataset of mean body size (carapace length) for extant whip spiders and a dated phylogeny. We also have data on the body size of fossil taxa. In geiger::fitContinuousMCMC it's easy to include that information as a root prior. But we also have intraspecific variation of body size for extant species, to which we calculated the standard error. It's easy to include that in geiger::fitContinuous. Question: We'd like to include both intraspecific variation and fossil body size as root prior while fitting alternative evolutionary models at once. Is there a way to do 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 | Evolution | Frontiers in Ecology and the Environment | Journal of Biogeography | Journal of Herpetology <https://journalofherpetology.com/> | PeerJ [[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] 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 submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > >1. DR metric of Jetz et al. 2012 (Susana Lopez) > > -- > > Message: 1 > Date: Fri, 29 May 2020 20:10:20 + > From: Susana Lopez > To: "r-sig-phylo@r-project.org" > Subject: [R-sig-phylo] DR metric of Jetz et al. 2012 > Message-ID: > < > ro1p152mb1211a012cd0ce864d0a58868ab...@ro1p152mb1211.lamp152.prod.outlook.com > > > > Content-Type: text/plain; charset="utf-8" > > Hello: > > I'm looking for a package/function that will implement the DR metric > (species-level lineage diversification rate) of Jetz et al. (2012). > > Any suggestions? > > Susy > > > [[alternative HTML version deleted]] > > > > > -- > > Subject: Digest Footer > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > -- > > End of R-sig-phylo Digest, Vol 148, Issue 7 > *** > [[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] 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:
https://stackoverflow.com/questions/31044922/confidence-intervals-of-loadings-in-principal-components-in-r
but since the phylogenenetic pca also requires a tree object, I'm not sure
how to get it. Here is my try:
getPrcStat <- function (samdf,vname,pcnum){
prcs <- phyl.pca(fish_tree,samdf, mode = "corr") # returns matrix
return(prcs$L[ vname,pcnum ]) # pick out the thing we need
}
bootEst <- function(df,d){
sampledDf <- df[ d, ] # resample dataframe
return(getPrcStat(sampledDf,"areahema",1))
}
bootOut <- boot(my_data_frame,bootEst,R=1)
I have tried with phytools::phylo.pca and also adephylo::ppca and nothing
seems to work.
Appreciate if anyone could help.
--
Sincerely,
Diogo Borges Provete, PhD
Personal web page
Assistant Professor
Department of Ecology
Institute of Biosciences
Federal University of Mato Grosso do Sul
University of Gothenburg
Gothenburg, Sweden
Skype: diogoprovete
Editor: Amphibia-Reptilia
[[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] 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 Sul Brazil Lab webpage <http://diogoprovete.weebly.com> ResearchGate <https://www.researchgate.net/profile/Diogo_Provete> Associated Member Gothenburg Global Biodiversity Centre <http://ggbc.gu.se> Box 462 SE-405 30 Göteborg, Sweden Cell phone: +5515981022137 Skype: diogoprovete Editor: Amphibia-Reptilia | Biodiversity Data Journal [[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] How to incorporate intraspecific variation in MCMCglmm
Dear list, I'm trying to fit a mixed-effects model to a problem that includes: a continuous response variable (mean jumped distance by 17 species of frogs) in 3 different arenas and under 2 types of stimuli. So, it's a kind of two-way ANOVA design. I have the species phylogeny and prepared its inverse: treeAinv<-inverseA(phylo,nodes="TIPS",scale=TRUE)$Ainv I included the following priors: prior = list(R = list(V = 1, fix = 1), G=list(G1=list(V=1, nu=0.02))) and the model: model1<-MCMCglmm(mean_distance~type_arena*type_of_stimulus, random=~Specie, data=df_spe, family="gaussian", ginverse = list(Specie=treeAinv), nodes="ALL", prior=prior, nitt=30, burnin=25000, thin = 100, verbose=FALSE) which seems to converge well (heidel.diag p-value = 0.428), ESS greater than 1000 for both random and fixed effects. My question is: how can I incorporate intraspecific variation in the jumped distance? I have the standard error of the distance and tried to make the model as: random=~Species+ us(1+se_distance):Species but I keep getting an error about prior specification: Error in MCMCglmm(mean_distance ~ type_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 São Carlos Sorocaba Gothenburg Global Biodiversity Centre Box 462 SE-405 30 Göteborg, Sverige diogoprovete.weebly.com Cell phone: +5515981022137 Skype: diogoprovete Editor: Amphibia-Reptilia | Biodiversity Data Journal [[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] 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 along the phylogeny. Does it make sense? Thank you in advance, Diogo -- Atenciosamente, *Diogo Borges Provete* == Biólogo Mestre em Biologia Animal (UNESP http://www.ibilce.unesp.br) Doutorando PPG Ecologia e Evolução http://www.ecoevol.ufg.br Laboratório de Ecologia de Insetos (sl. 222) Departamento de Ecologia http://www.icb.ufg.br/pages/18570 Instituto de Ciências Biológicas http://www.icb.ufg.br - ICB 1 Universidade Federal de Goiás http://www.ufg.br, campus II Goiânia-GO 74001-970 Brazil Tel. Lab. +55 62 3521-1732 *Cel. +55 *62 8231-5775 * *: diogoprovete *Personal web page http://diogoprovete.weebly.com* Editor Herpetology Noteshttp://www.herpetologynotes.seh-herpetology.org/index.html NorthWestern Journal of Zoologyhttp://biozoojournals.3x.ro/nwjz/index.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] 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, *Diogo Borges Provete* == Biólogo Mestre em Biologia Animal (UNESP) Doutorando PPG Ecologia e Evolução Laboratório de Ecologia de Insetos (sl. 222) Departamento de Ecologia Instituto de Ciências Biológicas - ICB 1 Universidade Federal de Goiás, campus II - UFG Goiânia-GO CP: 131 74001-970 Brazil Tel. Lab. +55 62 3521-1732 *Cel. +55 *62 8231-5775 * *: diogoprovete **: diogop...@yahoo.com.br *Personal web page https://sites.google.com/site/diogoprovetepage/* == [[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] 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 phylosor value and the randomized value? Thank you in advance and I'm sorry if this question is too simple. Diogo -- Atenciosamente, *Diogo Borges Provete* == Biólogo Mestre em Biologia Animal (UNESP) Doutorando PPG Ecologia e Evolução Laboratório de Ecologia de Insetos (sl. 222) Departamento de Ecologia Instituto de Ciências Biológicas - ICB 1 Universidade Federal de Goiás, campus II - UFG Goiânia-GO CP: 131 74001-970 Brazil Tel. Lab. +55 62 3521-1732 *Cel. +55 *62 8231-5775 * *: diogoprovete **: diogop...@yahoo.com.br *Personal web page https://sites.google.com/site/diogoprovetepage/* Traduza conosco: http://www.journalexperts.com/br/ Perfil no ProZ http://www.proz.com/profile/1335025http://www.proz.com/profile/1335025 == [[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 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 given organ 100% pigmented), being the intermediary categories defined as follows: 1% Category 1 50 % and 51% Category 2 100%]. I want to test for a phylogenetic autocorrelation of these discrete traits. I was considering the analysis proposed by Pavoine et al. (2008) of the Abouheif/Moran test (adephylo::abouheif.moran), but I'm not sure if I can include categorical traits. Additionally, the adjusted Mantel for phylogenetic permutation proposed by Harmon Glor (2010) seems also apropriated in this case. On the other hand, the method proposed by Pavoine et al. (2010) Ecol. Monog. allows for the decomposition of trait diversity along the tree nodes, but all the applications of this method I've seen were with continuous traits. Any idea on how to solve this dilemma? Thanks a lot, Diogo -- Atenciosamente, *Diogo Borges Provete* == Biólogo Mestre em Biologia Animal (UNESP) Doutorando PPG Ecologia e Evolução Laboratório de Ecologia de Insetos (sl. 222) Departamento de Ecologia Instituto de Ciências Biológicas - ICB 1 Universidade Federal de Goiás, campus II - UFG Goiânia-GO CP: 131 74001-970 Brazil Tel. Lab. +55 62 3521-1732 *Cel. +55 *62 8231-5775 * *: diogoprovete **: diogop...@yahoo.com.br *Personal web page https://sites.google.com/site/diogoprovetepage/* Traduza conosco: http://www.journalexperts.com/br/ D-Lang Soluções linguisticashttp://www.d-lang.com.br/site/sitept/index.htm Perfil no ProZ http://www.proz.com/profile/1335025http://www.proz.com/profile/1335025 == [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
