[R-sig-phylo] binary trait influencing diversification

the speciation rate of a branch at state 1. I tried to modify the functions I find in geiger and phytools, but I couldn't keep track of things during the simulation. Any suggestion would be fantastic. Karla Shikev [[alternative HTML version deleted]] ___ R

[R-sig-phylo] NNI/SPR Distance

Dear colleagues, Does anyone know of a function to calculate the NNI/SPR distance between two trees? Thanks a lot! Karla Shikev [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

Re: [R-sig-phylo] testing for variation in rates of evolution among traits

/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 Karla Shikev [karlashi...@gmail.com] Sent: Thursday, July 16, 2015 2:13 PM To: r-sig-phylo@r-project.org

[R-sig-phylo] testing for variation in rates of evolution among traits

Hi there, I've come across several methods to test for differences in the rate of evolution among branches in a tree, but I can't find methods to test for differences in rates of evolution of different traits on the same species (ex. if wing size evolution is faster than than overall body size

[R-sig-phylo] add.species.to.genus with pure birth branch lengths

Dear all, I need to add species go a genus-level phylogeny, such that the generated nodes are consistent with a Yule process. I tried phytools' add.species.to.genus function, but the generated branch lengths tend to be too recent. Any thoughts? Thanks, Karla. [[alternative HTML version

Re: [R-sig-phylo] add.species.to.genus with pure birth branch lengths

; University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > > On 10/27/2015 7:06 PM, Karla Shikev wrote: > >> Dear all, >> >> I need to add species go a genus-level phylogeny

[R-sig-phylo] Fwd: rate units in fitContinuous

nce of the OU process is sigsq^2/(2*alpha), thus if alpha is high > enough the stationary variance will tend towards 0, and all the traits > across taxa will be virtually identical). > > Hope this helps. > Josef Uyeda > > > > On 12/07/2015 03:35 PM, Karla Shikev wrote: > >

Re: [R-sig-phylo] Fwd: rate units in fitContinuous

g-phylo <r-sig-phylo-boun...@r-project.org> de la part de Karla > Shikev <karlashi...@gmail.com> > Envoyé : mardi 8 décembre 2015 11:57 > À : r-sig-phylo@r-project.org > Objet : [R-sig-phylo] Fwd: rate units in fitContinuous > > Thanks, Josef (and those that answ

[R-sig-phylo] rate units in fitContinuous

Dear all, I am fitting a BM model using fitContinuous, a vector of trait values and a time-calibrated tree and then I use the sigsq parameter as my measure of the rate of evolution of the trait in question. My questions are: (1) what is the unit of the sigsq parameter? (2) to what extent is the

[R-sig-phylo] concatenating loci with different taxa

Dear all, I got alignments for many loci as nexus files and I've been trying to concatenate them into a single alignment. However, some taxa are missing from some of the loci, so that simple alternatives such as cbinding individual files in phangorn doesn't work. Any help with this will be

[R-sig-phylo] distances between trees

Here's another question. I'm looking for ways to compute distances between two trees when there are differences in the sets of tip labels. Based on some preliminary tests using simulated trees, phangorn's RF.dist gives me exactly the same results as ape's dist.topo (which makes me wonder if

Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

p://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > > On 7/22/2017 3:10 PM, Karla Shikev wrote: > >> Dear all, >> >> I'd like to test whether the rate of evolution of a phenotypic trait (e.g. >> body siz

[R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

Dear all, I'd like to test whether the rate of evolution of a phenotypic trait (e.g. body size) is significantly different among distantly-related clades (e.g. mammals vs birds). I got tip data and completely resolved and callibrated trees. One possibility would be to estimate rates and their

[R-sig-phylo] AGY coding

Dear all, Does anyone have a function for AGY coding of nucleotides? By the way, any thoughts on using RY- vs AGY-coding? Thanks! Karla [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

Re: [R-sig-phylo] AGY coding

10.1186/1471-2105-15-S2-S8> > is very nice. Basically, if you are using them for phylogenetic inference > it may be that recoding destroys the Markovian property of the alignment, > and that may mislead you downstream. A very interesting consideration that > I feel is not widely known

Re: [R-sig-phylo] model averaging using brownie.lite

etts Boston > Profesor Asistente, Universidad Católica de la Ssma Concepción > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org > > Academic Director UMass Boston Chile Abroad (starting 2019): > https://www.umb.edu/academics/caps/international/biology_chile > > On 9/

[R-sig-phylo] model averaging using brownie.lite

Dear all, I've been trying to use brownie.lite to implement the tutorial available here (http://treethinkers.org/tutorials/morphological-evolution-in-r/) to calculate model-averaged rates of evolution and for model selection (1 versus 2 rates). However, the current version of phytools 0.6-99

Re: [R-sig-phylo] issue with add.species.to.genus

on of laser from > the CRAN repository on GitHub using devtools. That won't always be the > case, but I ran out of time to complete the project and it's currently a > dependency. > > Best wishes, > Eliot > > On Tue, Sep 24, 2019 at 5:42 PM Karla Shikev > wrote: > >

[R-sig-phylo] issue with add.species.to.genus

Dear all, Some time ago, Liam Revell kindly provided the code that is now incorporated into phytools in the add.species.to.genus function, which randomly adds an additional species to a genus on a phylogeny. However, this function either adds a species to the root node, or to the branches after

[R-sig-phylo] BD process in Nee et al. (1994)

Dear all, Does anyone know of a function in R which would provide the analytical solution to the expectation for the number of species over time derived by Nee et al. (1994, Phil. Trans. R. Soc. Lond B.)? Thanks, Karla [[alternative HTML version deleted]]

[R-sig-phylo] collapsing sets of nodes based on label values

Dear all, I'm surprised I could not find a simple function to do this in any of the packages I know. I just want to take a tree with node labels (e.g. bootstrap values from a RAxML analysis) and collapse all nodes with support values below, say, 90%. I tried to do this recursively using

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

r low measured >> values of phylogenetic signal. >> >> Hope this is of some help Karla. >> >> All the best, Liam >> >> Liam J. Revell >> University of Massachusetts Boston >> Universidad Católica de la Ssma Concepción >> web: http://faculty.u

[R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Dear friends, I guess this is as much a philosophical question as it is methodological. I want to estimate the rate of evolution of a trait (e.g. using the fitContinuous function), but the trait has low phylogenetic signal (e.g. lambda close to 0). Does it make sense to use fitContinuous on a

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

faculty.umb.edu/liam.revell/, http://www.phytools.org > > Academic Director UMass Boston Chile Abroad: > https://www.umb.edu/academics/caps/international/biology_chile > > On 9/23/2020 9:36 PM, Karla Shikev wrote: > > **[EXTERNAL SENDER] > > > > Dear All, &

[R-sig-phylo] regression slopes

Dear friends, What would be your suggestion for the best PCM to obtain "phylogenetically-corrected" slopes and intercepts of a relationship between two continuous variables? Karla [[alternative HTML version deleted]] ___ R-sig-phylo mailing

[R-sig-phylo] phylogenetic distribution of a continuous trait

Dear all, It is commonplace to look at the distribution of discrete characters (i.e. if they are overdispersed, clustered or randomly distributed). Is there a similar type of analysis for a continuous trait? thanks! Karla [[alternative HTML version deleted]]

Re: [R-sig-phylo] units of sigsq

e ven. 19 mars 2021 à 19:12, Karla Shikev a > écrit : > >> Dear all, >> >> Please indulge me in a simple (newbie) question. >> >> If I have a continuous trait (log(body size in g)) and a calibrated tree >> and use fitContinuous to estimate sigsq u

[R-sig-phylo] units of sigsq

Dear all, Please indulge me in a simple (newbie) question. If I have a continuous trait (log(body size in g)) and a calibrated tree and use fitContinuous to estimate sigsq using a BM model, what is the unit of the siqsq estimate? log(g)/My? Thanks for your patience, Karla

[R-sig-phylo] de Villemereuil et al. 2012 in R

Dear all, de Villemereuil et al. (2012) implemented an approach to account for phylogenetic uncertainty in PGLS using BUGS. Does anyone know of it being implemented in R? de Villemereuil, P., Wells, J. A., Edwards, R. D., & Blomberg, S. P. (2012). Bayesian models for comparative analysis

Re: [R-sig-phylo] de Villemereuil et al. 2012 in R

That is really cool! Thanks! On Wed, Mar 3, 2021 at 11:20 PM Simone Blomberg wrote: > Hi Karla, > > The code runs fine in JAGS so you can use rjags in R to fit the models. > > Cheers, > > Simone. > > On 3/3/21 11:24 pm, Karla Shikev wrote: > > Dear all, >

[R-sig-phylo] MK1 vs MK2 with phylogenetic uncertainty

Dear all, I'm planning on testing the relative fit of an MK1 model for the evolution of a discrete trait against a MK2 model (in this case, the ARD model in phytools). However, I'd like to take into account phylogenetic uncertainty, as I have a set of post-burnin trees. What would you guys

[R-sig-phylo] Estimating tip rates of molecular evolution

Dear all, I want to test for a relationship between interspecific rates of evolution and a continuous predictor variable. I didn't want to use species pairs because they end up looking a lot of information. The method implemented in Colevol is very elegant, but is computationally unfeasible with

[R-sig-phylo] estimating BLs on a fixed topology

Dear all, I have a large alignment (>3000 species) and a topology and I'd like to estimate branch lengths on that fixed topology using a GTR+G model, but it has been challenging computationally using optim.pml in phangorn. Any ideas about how to speed things up? Thanks! Karla