[R-sig-phylo] Multi-Predictor ANOVA?

like aov.phylo is not built to perform a multi-predictor analysis like the normal aov function is. Are there any similar functions that would be able pull this off? Is there way around this with aov.phylo? Any thoughts would be greatly appreciated, Will -- William Gearty PhD Student, Paleobiology

Re: [R-sig-phylo] Multi-Predictor ANOVA?

lty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > > On 2/4/2015 5:38 PM, William Gearty wrote: > >> Apologies if this has been asked before... >> I'm trying to perform a phylogenetic ANOVA with multiple predictors. >> I'

Re: [R-sig-phylo] Multi-Predictor ANOVA?

t term, the >> model becomes unidentifiable because you've effectively included two >> intercept terms which are additively non-identifiable. >> >> I hope that makes sense. >> >> Cheers, >> >> Peter >> >> On Wed, Feb 4, 2015 at 5:20 PM, Will

[R-sig-phylo] PGLS Anova Error

r workaround? Thanks once again in advance, Will -- William Gearty PhD Student, Paleobiology Department of Geological and Environmental Sciences Stanford School of Earth, Energy & Environmental Sciences people.stanford.edu/wgearty [[alternative HTML version deleted]] ___

[R-sig-phylo] (P)GLS (nlme) vs. PGLS (caper)

analyses? Should I feel okay about estimating all three Pagel parameters at the same time with PGLS? Any insight or thoughts would be greatly appreciated. Thanks, Will -- William Gearty PhD Student, Paleobiology Department of Geological and Environmental Sciences Stanford School of Ear

Re: [R-sig-phylo] PGLS Anova Error

variables. I've attached the fixed anova.pgls script here. It's been working for me and two other users confirm that it is working for them as well. If you do use the script and it solves your problems, please let me know. -Will On Sat, Mar 7, 2015 at 10:20 PM, William Gearty wrote: >

Re: [R-sig-phylo] Sister-clade analysis of discrete characters

__ > 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/ > -- William Gearty PhD Student, Paleobiology Department o

[R-sig-phylo] PGLS vs OUwie?

just point me in that direction. Thanks in advance, Will -- William Gearty PhD Student, Paleobiology Department of Geological Sciences Stanford School of Earth, Energy & Environmental Sciences people.stanford.edu/wgearty [[alternative HTML version del

Re: [R-sig-phylo] Pairwise genetic distances for many genes and taxa

> Florida State University > cbuddenha...@gmail.com > > [[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 > h

Re: [R-sig-phylo] Package phytools load failed

les University in Prague > > Benátská 2, Prague, 12801, CZ > > http://botany.natur.cuni.cz/en/ > > > > Institute of Botany, Academy of Science > > Zámek 1, Průhonice, 25243, CZ > > http://www.ibot.cas.cz/en/ > > > > Czech Republic > > > >

[R-sig-phylo] Convert Node Labels to Edge Labels

ry, please feel free to point me in that direction. Thanks in advance, Will -- William Gearty PhD Student, Paleobiology Department of Geological Sciences Stanford School of Earth, Energy & Environmental Sciences people.stanford.edu/wgearty [[alternative HTML v

Re: [R-sig-phylo] Supertree with Stratigraphic Constraints

Hmm, so I'll take it that this doesn't exist yet? On Thu, Sep 8, 2016 at 10:28 AM, William Gearty wrote: > Hi all, > > I'm currently working with a supertree to perform some comparative > analyses. > Of course, I have to time-scale the tree to perform the analys

Re: [R-sig-phylo] Supertree with Stratigraphic Constraints

nverting a tree in R > into a set of constraints for MrBayes. At least on paper, > character-less tip-dating should be like doing cal3... in practice, > though, I have no idea what will happen. Maybe it will have the same > problems as your cal3 trees, maybe it won't. > > I hope thi

[R-sig-phylo] MrBayes Branch Lengths in R

my MrBayes nexus file/analysis, which is causing the branch lengths to be off in the output file (I was under the impression branch lengths are by default printed with the trees)? Or is there a different (better) way to import them into R? Thanks in advance, Will -- William Gearty PhD Candidate, Pa

Re: [R-sig-phylo] MrBayes Branch Lengths in R

Resolved; I hadn't taken into account the fact that I needed to scale my trees by the clock rate. On Thu, Feb 16, 2017 at 4:32 PM, William Gearty wrote: > Hi all, > > I've recently finished a tip-dating analysis (see > https://www.mail-archive.com/r-sig-phylo@r-project.

[R-sig-phylo] Function to Extend Tips?

Hi all, Before I go ahead and wrote a whole script, I was wondering if there is a function or script out there for extending tips (or setting the ages of tips) given a list of taxa and ages? I haven't found anything, but perhaps I'm searching the wrong phrase(s). Thanks, Will -- Will

Re: [R-sig-phylo] Function to Extend Tips?

hat you mean by extending tips, Will. Could you describe a > small example? > -Dave > > On Fri, Jul 21, 2017 at 5:15 PM, William Gearty > wrote: > > Hi all, > > Before I go ahead and wrote a whole script, I was wondering if there is a > function or script out there f

Re: [R-sig-phylo] Function to Extend Tips?

} > > Probably a nicer way to do it without a loop... > > JWB > > Joseph W. Brown > Post-doctoral Researcher, Smith Laboratory > University of Michigan > Department of Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building &

[R-sig-phylo] Mean of Phenogram Through Time

r the different discrete character states? Thanks, Will -- William Gearty PhD Candidate, Paleobiology Department of Geological Sciences Stanford School of Earth, Energy & Environmental Sciences williamgearty.com [[alternative HTML versio

Re: [R-sig-phylo] Mean of Phenogram Through Time

Nevermind, figured it out! If you ever find yourself wanting to do this, I've attached my script here. On Tue, Feb 13, 2018 at 6:22 PM, William Gearty wrote: > Hi all, > > Perhaps I'm googling the wrong thing or just too tired to figure this out > myself, but is there

Re: [R-sig-phylo] Mean of Phenogram Through Time

Sorry, this time with comments! (and through spelled correctly) Happy to take any questions! On Tue, Feb 20, 2018 at 6:00 PM, William Gearty wrote: > Nevermind, figured it out! > If you ever find yourself wanting to do this, I've attached my script here. > > On Tue, Feb 13

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

s <https://twitter.com/brown_birds> > > > ___ > 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-ph..

Re: [R-sig-phylo] diversification rates

TML 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

Re: [R-sig-phylo] diversification rates with two traits present simultaneously

I'm not sure of any particular methods that do this, but one preliminary approach that you could try is combining the two traits into a single trait (00, 01, 10, and 11) which you could then analyze with any of the standard methods. You could then look for whether any of the states have higher or l

Re: [R-sig-phylo] Adding species to genera tree as polytomies

_ > 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/ > -- William Gearty PhD Candidate, Paleobiology De

Re: [R-sig-phylo] comparePhylo

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/ > -- William Gearty PhD Candidate, Paleobiology Department of Geological Sciences Stanford School of E

Re: [R-sig-phylo] data violate assumptions of PGLS

One option that I can think of is to code the binary trait at the genus level (it sounds like this should be fairly simple for most of them, then maybe use a cutoff for the rest) and then do a phylogenetic logistic regression (e.g. using phylolm)? On Sat, Jul 20, 2019, 1:15 PM Elizabeth Christina

Re: [R-sig-phylo] p-value of PGLS models in caper

It looks like the p-value is calculated as follows: pf(summ$fstatistic[1], summ$fstatistic[2], summ$fstatistic[3], lower.tail = FALSE) You can format it like it is in the summary by wrapping that in format.pval(). Best, Will William Gearty williamgearty.com On Tue, Dec 10, 2019 at 1:33 PM

[R-sig-phylo] Multivariate ASR with Discrete Characters

this will never exist for computational or theoretical reasons? Thanks in advance, Will *William Gearty* Postdoctoral Research Fellow University of Nebraska–Lincoln School of Biological Sciences williamgearty.com [[alternative HTML version deleted]] __

Re: [R-sig-phylo] Multivariate ASR with Discrete Characters

te (1) characters? I see that phytools has ancThresh, but that only seems to work with a single character. I also believe I found Goolsby's model/software <https://github.com/nspope/epee> that Julien alluded to, but it doesn't seem to be ready for primetime yet. Thanks, Will *William

Re: [R-sig-phylo] Highlighting Specific Clades in a Lineage-Through-Time Plot

You could also map your states (in this case, taxonomic groupings) onto your tree, then make an ltt plot with phytools::ltt(). Liam has a great blog post about it here: http://blog.phytools.org/2022/08/lineage-through-time-plots-for.html. Best, Will -- *William Gearty

Re: [R-sig-phylo] Highlighting Specific Clades in a Lineage-Through-Time Plot

retty close to what I am looking for. > > Emmanuel's suggestion of using ltt.plots.coords might also work, and it > might be easier to input that data into ggplot if I could find some way to > merge the various matrices. > > Russell > > On Fri, Oct 27, 2023 at 10:04 AM