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

One way to do it with pGLS and root to tip path length may be to include the number of nodes along a root to tip path as a control for node density effects (maybe with some transformation). I don't know how well that will work, but I am also experimenting with similar questions. Another way is to

Re: [R-sig-phylo] Data normalization

Interesting thought. I am not familiar with these analyses, but it would not surprise me if your intuition is correct. J > On Sep 19, 2021, at 1:00 PM, Ferenc Tibor Kagan wrote: > > Dear r-sig-phylo community > > I am writing to you in hopes of you giving me your inputs on a specific topic.

Re: [R-sig-phylo] Ancestral state reconstruction, polytomies and the absence of branch lengths

Hi Diego, If your tree has polytomies and the branches have no length information, I am not sure if likelihood model-based reconstruction is right. The ace function (and all other similar functions based on likelihood) will assume that your branch lengths represent some kind biological

[R-sig-phylo] identifying phylogenetically equivalent nodes

Dear R-sig-phylo, Over the weekend, I asked Liam Revell if he had a solution to use matchNodes for a particular problem I’m trying to solve—finding all phylogenetically equivalent nodes when comparing trees that have uneven taxon samples and different topologies. Liam was kind enough to take

Re: [R-sig-phylo] model averaging for discrete character evolution

Accidentally replied directly to Marguerite, instead of to the list: > On Aug 9, 2019, at 10:01 AM, Jacob Berv > wrote: > > Great points Marguerite. I agree that the idea of using ‘all possible’ models > is probably a bit too overzealous— and as Brian pointed o

Re: [R-sig-phylo] model averaging for discrete character evolution

n > web: http://faculty.umb.edu/liam.revell/ > <http://faculty.umb.edu/liam.revell/>, http://www.phytools.org > <http://www.phytools.org/> > > Academic Director UMass Boston Chile Abroad (starting 2019): > https://www.umb.edu/academics/caps/international/biology_chile >

[R-sig-phylo] model averaging for discrete character evolution

Dear R-sig phylo I’ve been running a few discrete character Mk type models using phytool's SIMMAP — and I had the idea that it might be useful to try model averaging across posterior probabilities for node states. Might this make sense to do, to avoid problems associated with model ranking

Re: [R-sig-phylo] aov.phylo vs phylANOVA

Sorry— I meant aov.phylo (geiger function), not phly.aov. J > On Nov 15, 2018, at 3:00 PM, Jacob Berv > wrote: > > Hi everyone — > It seems like the solution is that I was looking at the wrong p-value, as is > often the case! > > From Liam: > "The is

Re: [R-sig-phylo] aov.phylo vs phylANOVA

end along the data that has generated this incongruency if you are > unable to figure it out. > > All the best, Liam > > Liam J. Revell > Associate Professor, University of Massachusetts Boston > Profesor Asistente, Universidad Católica de la Ssma Concepción > web: http://f

[R-sig-phylo] aov.phylo vs phylANOVA

Dear R-sig-phylo, I was wondering if anyone on here might be able to help me understand the difference between phytool’s implementation of phylogenetic ANOVA and geiger’s implementation. From the respective documentation, it seems that both approaches rely on and cite the same reference:

Re: [R-sig-phylo] plot heatmap at nodes

> All the best, Liam > > Liam J. Revell > Associate Professor, University of Massachusetts Boston > Profesor Asistente, Universidad Católica de la Ssma Concepción > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org > > On 8/29/2018 7:12 PM, Jacob Berv wr

[R-sig-phylo] plot heatmap at nodes

Dear R-sig-phylo, Does there exist a function to plot heatmaps at internal nodes of a tree? For example, to illustrate support values from different phylogenetic analyses — ie given a set of 3x3 matricies of support values for particular nodes. It seems like there may be a partial (and

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

This is so cool. Thanks Liam! J > On Jun 21, 2018, at 8:22 PM, Liam J. Revell wrote: > > Dear Theo. > > This can be done with the function rerootingMethod as described here > http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html, > although it is *very* important to note

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

What about situations in which fossil calibrations are used as priors to inform reconstructions for uncalibrated important/interesting nodes? Sure, there is great uncertainty, but that doesn’t necessarily imply we should entirely abandon hypothesis testing using this approach, does it? I like

Re: [R-sig-phylo] "Not of class phylo" error when lapply is used

This is cool — so this looks like it will work on a set of posterior trees even if they don’t all share the same topology? Jake > On Apr 10, 2018, at 3:37 AM, jschenk wrote: > > Thank you Graham, Liam, and Emmanuel for your suggestions. Applying the >

Re: [R-sig-phylo] Interpretation of standard errors of parameter estimates in OUwie models

Even if those models may fit the data better, they may not necessarily help Rafael determine whether or not the parameter estimates of interest are different across regimes (though perhaps BMS might be informative). Rafael, maybe you could try fixing the ancestral regimes to match most likely

[R-sig-phylo] plotting geologic time scale on circular tree

Hi all, Does anyone know of a function to plot a geologic time scale as a series of concentric circles on a circularly plotted tree? As far as I can tell there are three available functions that can do this on a regular cladogram: axisGeo (phyloch) geoscale.Phylo (strap) geo.legend (phytools)

Re: [R-sig-phylo] Rooting trees in R

see root() in the R package ape or reroot() in phytools J > On May 23, 2017, at 1:22 PM, Valentine Usongo > wrote: > > Dear members > > My name is Valentine Usongo and I am a postdoctoral trainee at the INSPQ > Montreal-Quebec. I am working on the use of whole

Re: [R-sig-phylo] Graphically comparing multiple trees

Very interested in this too! Jake > On Apr 25, 2017, at 1:20 PM, Vojtěch Zeisek wrote: > > Hello, > for comparison of two trees I can use very nice function cophyloplot plotting > two trees (left and right) and connecting respective nodes by lines. Very > nice > and

[R-sig-phylo] phylip file compression ratios

I noticed today that the compression ratio for an interleaved phylip file (zip compressed) was about 84:1, (390MB uncompressed —> 4.6MB compressed) whereas the compression ratio for the same data non-interleaved was a much worse 3.4:1 (390 MB uncompressed —> 113.9 MB). Not knowing much about

[R-sig-phylo] computing phylogenetic residuals

Hi all, I’m trying to compute size corrected phylogenetic residuals on data where the independent variable (size) is complete but the dependent variables have varying amounts of missing data. phyl.resid() in phytools doesn’t appear to be able to handle pairwise dropping (to only consider rows

Re: [R-sig-phylo] HKY GTR distances

Can you do this in MEGA? Jake > On Feb 1, 2017, at 5:52 PM, kolte...@rub.de > wrote: > > Dear Phylothusiasts, > I need to compare multiple substitution models side-by-side (species > clustering stuff by distances only). Unfortunately, I am not aware of an >

Re: [R-sig-phylo] to log or not to log

ing this is some sort of regression model (i.e., you have one or more > independent variables), then you CAN look at residuals to see if they are > better/worse behaved (e.g., approximately normal, no nasty outliers, > homoscedasticity). > > Cheers, > Ted > > > On Thu,

[R-sig-phylo] to log or not to log

Dear R-sig-phylo, When analyzing comparative data in a PCM framework, is it be appropriate to use an AIC score to advocate for log transforming input data? ie model(data) vs model(log(data)) I’m running a few OUwie models and it’s not entirely clear from the biology whether or not the

Re: [R-sig-phylo] Comparing support values on different trees

To clarify - the idea here is that you are asking which clades appear in ’subordinate’ trees relative to clades that exist in a consensus tree, and then interrogating the support values of the shared clades which exist in the ’subordinate’ trees? So for example, clade A appears in consensus

Re: [R-sig-phylo] Use of a Phylocom tree for PGLS

Personally, I don’t think I’d have a problem with this approach (especially given the paper Liam cited) given that you are using a phylogeny (a model) to test a hypothesis, which is, after all, all we can ever do. You can always do more, so any threshold of phylogenetic tree “quality” is going

Re: [R-sig-phylo] suppress axes in phenogram()

My ugly solution is to comment out lines 195 and 196 in the phenogram code. Jake > On Jul 7, 2016, at 5:06 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com> wrote: > > Cool - that works - but now I can’t use axis() to add custom axes… > Jake > >> On Jul 7, 2016,

[R-sig-phylo] suppress axes in phenogram()

Hi all, Does anyone know if there is an easy way to suppress the axes in phytools phenogram() without altering the code (which is easy to do, but inconvenient when using the function in multiple different contexts)? yaxt=’n’ and xaxt=’n’ have no effect. Best, Jacob Berv

Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?]

Also see BayesTraits for the bayesian version. Jake > On May 3, 2016, at 8:11 PM, Liam J. Revell wrote: > > Hi Michael. > > This is essentially the method of Pagel (1994). Though often interpreted as a > test for correlated evolution of two binary characters, the model

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 95, Issue 6

There appears to be some issues with ggtree plotting BEAST output - I just tried to run through the example and got the following errors: source("https://bioconductor.org/biocLite.R;) biocLite("ggtree") require("ggtree") > file <- system.file("extdata/BEAST", "beast_mcc.tree",

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 95, Issue 6

Whoops! nevermind. It appears read.beast was being masked from read.beast in phyloch. Working now. Jake > On Dec 11, 2015, at 12:56 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com> > wrote: > > There appears to be some issues with ggtree plotting BEAST output - I just >

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

, substitution rate information). I emailed the developer of that tool and he indicated this was by design (though he may be able to offer a solution). Jake > On Oct 18, 2015, at 12:04 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com> > wrote: > > Yes, this has come up in my re

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

ate is independent of > the effective population size? > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

os.org/postdocs/ > <http://nimbios.org/postdocs/> > Calendar: http://www.brianomeara.info/calendars/omeara > <http://www.brianomeara.info/calendars/omeara> > On Sat, Oct 17, 2015 at 10:12 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com > <mailto:jakeberv.r.sig.ph...@gmail.com>&

[R-sig-phylo] simulate Ne changes on a given phylogeny

m. Any thoughts would be appreciated! Thanks, Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/list

Re: [R-sig-phylo] rotate nodes to match taxonomic order

, at 10:57 AM, Emmanuel Paradis emmanuel.para...@ird.fr wrote: Hi Jacob, Can you send an example of your output with rotateConstr()? Thanks. Best, Emmanuel Le 08/04/2015 06:41, Jacob Berv a écrit : Hi all, Is there an easy way to get R to automatically rotate the nodes of a phylogeny

Re: [R-sig-phylo] multipage pdf of a huge tree

/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

Re: [R-sig-phylo] multipage pdf of a huge tree

://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 3/5/2015 2:24 PM, Jacob Berv wrote: Hi Liam, Would there be a way to modify this so that annotations like node labels and axes could be applied to both 1/2s of a split tree at the same time? I’ve been

Re: [R-sig-phylo] multipage pdf of a huge tree

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 3/5/2015 2:24 PM, Jacob Berv wrote: Hi Liam, Would there be a way to modify this so that annotations

[R-sig-phylo] axisChrono and axisPhylo

argument “at matched by multiple actual arguments Does anyone know how I might be able to specify the tick marks that I want for these particular functions? Best, Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology ___ R-sig-phylo mailing

Re: [R-sig-phylo] axisChrono and axisPhylo

you have to alter the 'axisPhylo' function so you can define your own 'axis' at arguments. Hope that helps and is correct... Best Franz p.s. that's my first answer here but I feel today is a god day to start (thanks Dave Bapst for encouraging ;-)) Jacob Berv jakeberv.r.sig.ph

Re: [R-sig-phylo] axisChrono and axisPhylo

, at 11:10 PM, Santiago Claramunt sclaram...@amnh.org wrote: axis(1, at=max(branching.times(tree))-0:10, labels=0:10) Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology [[alternative HTML version deleted]] ___ R-sig-phylo