Re: [R-sig-phylo] Determining Order of Trait Evolution

I've read the hOUwie paper, but it wasn't clear to me that it allowed estimating the *order* of changes. Thanks, -Rafa *--* *Rafael S. Marcondes, Ph.D.* *https://www.rafaelmarcondes.com/ <https://www.rafaelmarcondes.com/>* Faculty Fellow in EEB Department of BioSciences Rice Un

Re: [R-sig-phylo] Determining Order of Trait Evolution

little overlap with the random distribution, that would indicate that changes in [redacted continuous-valued] morphology tend instead to follow changes in [redacted discrete valued ecology]. Thanks! -Rafa *--* *Rafael S. Marcondes, Ph.D.* *https://www.rafaelmarcondes.com/ <https://www.r

Re: [R-sig-phylo] Using results of make.simmap to color edges by most likely state

Thanks, Liam! It worked perfectly. -Rafa *--* *Rafael S. Marcondes, Ph.D.* *https://www.rafaelmarcondes.com/ <https://www.rafaelmarcondes.com/>* Faculty Fellow in EEB Department of BioSciences Rice University Houston TX 77005 Pronouns: he/him *"Eu quase que nada não sei. Mas d

[R-sig-phylo] Using results of make.simmap to color edges by most likely state

t; the likelihoods of different states into a single most likely state, and I absolutely do not plan to discard that uncertainty. I just want to plot a simpler tree for visualization. Thanks! -Rafa *--* *Rafael S. Marcondes, Ph.D.* *https://www.rafaelmarcondes.com/ <https://www.rafaelma

Re: [R-sig-phylo] Recovering rate estimates from ape::ace

matrix(fitMk(tree,x,model="ARD")) > > with phytools. > > All the best, Liam > > Liam J. Revell > University of Massachusetts Boston [Assoc. Prof.] > Universidad Católica de la Ssma Concepción [Adj. Res.] > > On 6/7/2021 6:52 PM, Rafael S Marcondes wrote: > &

[R-sig-phylo] Recovering rate estimates from ape::ace

Hi all, I'm very confused trying to understand the output of ace::ape, specifically the transition rates. I'm having a hard time understanding how the rates are stored in the results. For example, I used an ARD model on a trait with three states, denoted just 0, 1 and 2. I know that the rates ar

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

n > format.pval(). > > Best, > Will > > *William Gearty* > > Postdoctoral Research Fellow > > University of Nebraska–Lincoln > > School of Biological Sciences > > williamgearty.com > > > On Tue, Dec 10, 2019 at 1:33 PM Rafael S Marcondes < > raf.ma

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

Hi all, I'm having a hard time figuring out how to extract the p-value from a PGLS model fitted in caper. When I run summary(mod) and print it, I get, among other things: >summ=summary(mod) >summ Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept)0.0179553 0.0243

[R-sig-phylo] Number of parameters in BM and OU models in OUwie

Hi all, I'm trying to understand the number of parameters in simple BM and OU models in OUwie. $param.count in the fitted results gives 2 for BM and 3 for OU. I know that the 2 BM params are sigma and the trait value at the root, but I'm a little confused about the OU params. I expected there to b

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

Hi Elliot et al, Thanks for all the helpful answers, and sorry for my delay in getting back. min(tree$edge.length) returns a nonzero positive number, but running force.ultrametric on the tr did not cause that warning message to go away... *--* *Rafael Sobral Marcondes* PhD Candidate (Systematics

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

ondes* PhD Candidate (Systematics, Ecology and Evolution/Ornithology) Museum of Natural Science <http://sites01.lsu.edu/wp/mns/> Louisiana State University 119 Foster Hall Baton Rouge, LA 70803, USA Twitter: @brown_birds <https://twitter.com/brown_birds> On Wed, May 2, 2018 at

[R-sig-phylo] Problem with negative ages in OUwie.boot?

Hi all, I need some help with a warning message I've been getting when running parametric bootstrapping in OUwie. >OUwie.boot(nboot=1, simmap.tree=F...) Beginning parametric bootstrap -- performing 1 replicates Warning: Some dates are negative? rootAge may be incorrectly defined or you are using

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

y suitable. > > Best, > Will > > On Wed, Apr 4, 2018 at 12:30 PM, Rafael S Marcondes < > raf.marcon...@gmail.com> wrote: > >> Dear all, >> >> I'm writing (again!) to ask for help interpreting standard errors of >> parameter estimates in O

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

Dear all, I'm writing (again!) to ask for help interpreting standard errors of parameter estimates in OUwie models. I'm using OUwie to examine how the evolution of bird plumage color varies across habitat types (my selective regimes) in a tree of 229 tips. I was hoping to be able to make inferenc

Re: [R-sig-phylo] Phylogenetic PCA and measurement error

-- > > Graham J. Slater > > Assistant Professor > > Department of the Geophysical Sciences > > University of Chicago > > 5734 S. Ellis Avenue > > Chicago, IL 60637 USA > > > > Tel: (773) 702-0249 > > email: gsla...@uchicago.edu <m

[R-sig-phylo] Phylogenetic PCA and measurement error

Dear all, Does anyone have any advice on how to calculate measurement error in an analysis using phylogenetic principal components? Or, in other words, after I run a phylogenetic PCA on species-level data, how can I "project" my individual-level data into the phylogenetic PCs so I can calculate a

Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

d obtain something that makes sense. > > 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 > > On 11/10/20

[R-sig-phylo] Error in plotTree.wBars() in phytools

Hi all, I'm encountering a little bump trying to use this really cool plot function in phytools and I can't figure out what's wrong: > plotTree.wBars(tree=tr, x=dat) Error in plot.window(xlim = xlim, ylim = ylim, asp = asp) : need finite 'xlim' values Including an xlim argument doesn't work: >

[R-sig-phylo] Interpretation of lambda=1 (measurement error?)

Hi all, I’m calculating lambda (as a measure of phylogenetic signal) for a dataset of bird plumage color traits across a clade of ~400 species. However, for a few of the traits, the lambda estimate is 1.00. This happens both with phytools::phylosginal and with geiger::fitContinuous(model=‘lamb

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

f_crow 4.393245NA 1 1.1493008 *--* *Rafael Sobral Marcondes* PhD Candidate (Systematics, Ecology and Evolution/Ornithology) Museum of Natural Science <http://sites01.lsu.edu/wp/mns/> Louisiana State University 119 Foster Hall Baton Rouge, LA 70803, USA Twitter: @rafmarcondes

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

-fitting methods > that take species mean standard errors. > > 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.or

[R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi all, I’m using OUwie to fit multi-optima OU models and I have a question about incorporating measurement error into my analyses. I’m running my models with known measurement error (mserr=‘known’) and using the standard error (std.error()) as an estimate of it, as recommended by Ives et al (200