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

://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'm able to do a normal ANOVA with multiple predictors like this: aov(Y ~ X1 * X2, data) However, I'd like to account

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

. I hope that makes sense. Cheers, Peter On Wed, Feb 4, 2015 at 5:20 PM, William Gearty wgea...@stanford.edu wrote: Hi Liam, Thanks for the help! Does this type of linear model work if X1 and X2 are categorical variables? -Will On Wed, Feb 4, 2015 at 2:48 PM, Liam J. Revell liam.rev

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

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 Earth, Energy Environmental Sciences

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

. 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 wgea...@stanford.edu wrote: Hi

[R-sig-phylo] PGLS Anova Error

, 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 mailing list - R

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

-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 of Geological and Environmental Sciences Stanford School of Earth, Energy Environmental Sciences

[R-sig-phylo] PGLS vs OUwie?

to 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 deleted

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

; Charles 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/ > > > > Czec

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

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 version del

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 <wgea...@stanford.edu> wrote: > Hi all, > > I've recently finished a tip-dating analysis (see > https://www.mail-archive.com/r-sig-p

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

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, Paleobiology

[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 -- William Gearty

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

com> wrote: > > Not sure what you mean by extending tips, Will. Could you describe a > small example? > -Dave > > On Fri, Jul 21, 2017 at 5:15 PM, William Gearty <wgea...@stanford.edu> > wrote: > > Hi all, > > Before I go ahead and wrote a whole script,

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

lding > Ann Arbor MI 48109-1079 > josep...@umich.edu > > > > On 26 Jul, 2017, at 11:57, William Gearty <wgea...@stanford.edu> wrote: > > That's definitely helpful, Joseph, but I'll need to extend the tips to > varying amounts. > > Basically, I performed a tip-dati

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

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

for 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 version del

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 <wgea...@stanford.edu> wrote: > Hi all, > > Perhaps I'm googling the wrong thing or just too tired to figure th

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 <wgea...@stanford.edu> wrote: > Nevermind, figured it out! > If you ever find yourself wanting to do this, I've attached my script here. >

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

ps://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...@r-project

Re: [R-sig-phylo] diversification rates

n 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-ph...@r-p

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 Departm

Re: [R-sig-phylo] comparePhylo

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 Earth, Energy &a

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

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

) 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 Gearty* Postdo

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

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 William G