Re: [R-sig-phylo] tree thievery

tagging? keyboard shortcuts for Save (Ctrl-S), Save As (Ctrl-A)? built-in documentation? plot(newtree2) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Brian O'Meara

[R-sig-phylo] Fwd: Other: Software.GLMM_R_package

. Thanks, Jarrod Jarrod Hadfield j.hadfi...@ed.ac.uk Brian O'Meara NESCent Durham, NC http://www.brianomeara.info [[alternative HTML version deleted]] ___ R-sig-phylo mailing

Re: [R-sig-phylo] Phylogenetic reference trees

There's not yet a good single source. TreeBase.org has some topologies, but not all studies go in there yet. The largest one I know of there has 1569 taxa . The PhyLoTA browser (http://loco.biosci.arizona.edu/pb/ ) has trees for many groups and also allows you to download aligned data to

Re: [R-sig-phylo] Bayesian dating in R vs. Multidivtime

/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Brian O'Meara http://www.brianomeara.info Assistant Prof. Dept. Ecology Evolutionary Biology U

[R-sig-phylo] plot.phylo leftwards in ape

elsewhere (I'll keep poking around at it), but I wanted to point out the potential x.lim+direction=l bug in any case. I'm using ape 2.5. Thanks, Brian -- Brian O'Meara http://www.brianomeara.info Assistant Prof. Dept. Ecology Evolutionary

Re: [R-sig-phylo] estimate likelihood of data for given model and parameters

I have code for this in my TreEvo package (on R-forge -- see brownieneglnL in http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/R/brownie.R?rev=2root=treevoview=markup ) though note that the package itself is not all cleaned up into install.packages()-ready form. You could also dig

Re: [R-sig-phylo] Fst - DNA sequence data

-- ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website

Re: [R-sig-phylo] Model-Selection vs. Finding Models that Fit Well

___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Funding wanted: Want to collaborate

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

developers would use R's built-in debugging functions like browser(), debug(), and trace()]. Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications

Re: [R-sig-phylo] Convert instantaneous transition rate to time.

to measure this. In practice, I bet all these measures are pretty highly correlated and so which one is used might not have much practical importance, though this would be worth investigating if actual conclusions depend on the results. Best, Brian ___ Brian

Re: [R-sig-phylo] Estimating MRCA dates

on CRAN) with just a couple of commands. An updated version should be coming out later today (and if someone notices other things missing, please let me know). Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee

Re: [R-sig-phylo] variation in rates over time

) independently arrived at essentially the same method, so it is worth reading both papers. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications

Re: [R-sig-phylo] estimating mutation rates

might constrain the molecular tree to have the same proportional branch lengths as the chronogram. Look at pml() in phangorn for calculating the likelihoods. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee

Re: [R-sig-phylo] Why no branch lengths on consensus trees?

, Brian PS: Note that I am actively looking for grad students: info at http://www.brianomeara.info/lab . Guaranteed five years support, subject to decent performance. ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee

Re: [R-sig-phylo] Analysis with Multiple cores on Mac Workstation

(as most of us do) rather than apply functions, the foreach package combined with doMC is another easy way: there's a good vignette for this at http://cran.r-project.org/web/packages/doMC/vignettes/gettingstartedMC.pdf. Best, Brian ___ Brian O'Meara Assistant

Re: [R-sig-phylo] R Dendrograms for Subclones in a Somatic Cell Population: Time Interval Sampling.

this helps, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar

Re: [R-sig-phylo] Estimating ancestral states of a trait under selection

based on your knowledge of the climate then and then do a Bayesian reconstruction. I don't know of any packages that do this at the moment, but it wouldn't be hard to write. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U

Re: [R-sig-phylo] question about analysing trait differences

this but can't find it at the moment, but it's not hard to write -- post again if you need help with it and no better ideas have been proposed. Hope this helps, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee

[R-sig-phylo] R postdoc with O'Meara and Carstens

and Diversity. ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar

Re: [R-sig-phylo] Difficulty getting posterior probabilities into ape?

Phyloch has never been on CRAN as far as I know, but you can get it from http://www.christophheibl.de/Rpackages.html . Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http

Re: [R-sig-phylo] obtaining reasonable values from OUCH

___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info

Re: [R-sig-phylo] Count Deep Coal in R?

___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http

Re: [R-sig-phylo] Pairwise tree distance matrix

just call Mesquite functions. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check

Re: [R-sig-phylo] trouble estimating lambda with fitDiscrete

___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http

Re: [R-sig-phylo] compar.ou (sandra goutte)

___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara

Re: [R-sig-phylo] compar.ou

being pulled from CRAN by the CRAN maintainers until we resolved the difference). Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15

Re: [R-sig-phylo] Error in OUwie

that's true in this case) or are inactive. One other advantage of R-sig-phylo posts for help is that you're more likely to hear about other package alternatives (i.e., Have you tried mvSLOUCH or OUCH instead?). Best, Brian ___ Brian O'Meara Assistant Professor

Re: [R-sig-phylo] compar.ou

or amount of molecular change?). Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check

Re: [R-sig-phylo] OUwie diagn=T Error in dim(edges)

-project.org/scm/viewvc.php/*checkout*/pkg/R/OUwie.contour.R?revision=133root=ouwie. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due

Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the same function

There are at least three packages to do this: OUCH, SLOUCH, and OUwie. OUCH and OUwie are on CRAN; for SLOUCH, go to http://freshpond.org/software/SLOUCH/ . Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U

Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the same function

frequently, plus for developers it lets you see how often your packages are downloaded. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

sampling (even from taxonomic bias, of not separating two populations into different species until they are different enough) could have an effect. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee

[R-sig-phylo] Tree-for-all hackathon

://www.opentreeoflife.org [2] http://www.arborworkflows.com/ [3] http://www.evoio.org/wiki/HIP (Hackathons, Interoperability, Phylogenies) ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http

Re: [R-sig-phylo] tip order in phylogeny - How does it work?

Look at reorder.phylo() in ape and reorder() in phylo4: your desired tip order may be there. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators

Re: [R-sig-phylo] fitDiscrete across multiple datasets

to teach now. Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars

Re: [R-sig-phylo] fitDiscrete across multiple datasets

for tree inference for years, just not for comparative methods as much. In general, I like Ben's idea to use multiple characters to get at shared rates; we should see more of this. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary

Re: [R-sig-phylo] assign multiple discrete states to single tip

and white, but a character red+white), you'd need to do as Liam suggests and create a polymorphic trait and an ordered state matrix. This is possible in ace() in ape, rayDISC() in corHMM, and probably others. Best, Brian ___ Brian O'Meara Assistant Professor

Re: [R-sig-phylo] Unsual values of alpha in OU models

, so you cherry picked a different model to get the result you want). Hope this helps, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http

Re: [R-sig-phylo] ancestor vs. change plots

for the other trait (i.e., mouth volume) on the branches painted in different states (and seeing if these rates are biologically and statistically significantly different). Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

the general problem, but it can help in a pinch. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http

Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape)

, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Jun

Re: [R-sig-phylo] clade-specific release and radiate model?

Hi, Daniel. It's a bit arguable whether as alpha - 0, OU - BM: I think it should, but IIRC in OUCH this doesn't happen, and that's a deliberate choice. That said, I think that an OU with alpha near zero would be ok for your question, though you might want to think about how to penalize parameters

Re: [R-sig-phylo] corDISC binary coding problems

if they incorporate sampling frequency. Hope this helps. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs

Re: [R-sig-phylo] Ancestral Reconstruction with Polymorphic States

(i.e., a polymorphic species with 01 speciates by separating into a 0 monomorphic species and a 1 monomorphic species). Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http

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

Dick Hudson's ms software can simulate gene trees along a species tree or network with migration, changing population size, etc. The package phyclust can call ms. You could then just simulate nucleotides on these gene trees. Best, Brian ___ Brian O'Meara

Re: [R-sig-phylo] Fitting Brownian evolution with bounds

___ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Mon, Nov 30, 2015 at 4:18 AM, saurabh <

Re: [R-sig-phylo] Accounting for phylogeny in binary predictor, binary response data

http://sysbio.oxfordjournals.org/content/64/1/127 . Best, Brian ___ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calend

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

t we'll ever get to the point where we can make strong conclusions from a few changes. Best, Brian _______ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info On Tue, May 3, 2016 at 8:

Re: [R-sig-phylo] estimating the evolutionary rate of a continous trait

patterns: the correlation structure of interspecific data. Evolution 50:1404-1417. ___ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info On Fri, Apr 15, 2016 at 10:20 AM, Belinda K

Re: [R-sig-phylo] Chronos function in ape

Geiger has congruify functions that can use pathd8 to make a tree ultrametric (perhaps using an external chronogram to date it). There's some code in there to use r8s, as well, but it takes some digging. Best, Brian ___ Brian O'Meara Associate Professor Dept

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

hope your results are robust to any of these suggestions for tweaks. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomear

Re: [R-sig-phylo] Query about Phylogenetics in R

est, Brian _______ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/>

Re: [R-sig-phylo] Standard errors of theta estimates in OU models

is treated as annoying noise to a meaningful signal. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Fe

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

in the future. But it does give me an incentive to say, "get a better tree", so take that into consideration. Best, Brian _______ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.i

Re: [R-sig-phylo] How to test stratification of sampling across tree?

it actually works]. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/te

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

does ancestral state estimation, too, but I don't think all the models you want will be in the set. Could be adequate to answering the biological question, though. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especi

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

state 3 (aka binary states 10) has highest diversification rate) is consistent across the clades could be a good way of seeing if there are some kinds of heterogeneity that matter. Best, Brian ___ Brian O'Meara, http://www.bria

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

On Wed, May 2, 2018 at 2:53 PM, David Bapst wrote: > Given that your tree appears to be non-ultrametric enough to cause > branching.times to throw some nonsensical node ages, if it is supposed > to be ultrametric. I recommend checking it carefully to figure out why > the tips

Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny

, first): relevant paper Criscuolo, A., Berry, V., Douzery, E. J. P. , and Gascuel, O. (2006) SDM: A fast distance-based approach for (super)tree building in phylogenomics. Systematic Biology, 55, 740–755. Best, Brian ___ Brian O'Meara

Re: [R-sig-phylo] understanding variance-covariance matrix

. These approaches should get the same results, though the shared history on the tree approach is faster. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/&g

Re: [R-sig-phylo] keeping states discrete when plotting HiSSE results

lwd=edge.width.state, legend=FALSE, type=type, fsize=fsize, ...) Hope this helps, Brian ___________ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://briano

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

/data["alpha", traits[trait.index]], 2))) cat(paste0("\nTree height: ", round(max(ape::branching.times(bla$phy)),2))) } points.to.plot <- bla$data[,1:2] colnames(points.to.plot) <- c("regime", "trait1") beeswarm(trait1~regime, data=points.to.plot, col="black&qu

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

Apparently the plot did not come through correctly. I'm attaching a PDF of it. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV

Re: [R-sig-phylo] quantitative state dependent diversification of another quantitative trait

I think you want SLOUCH: Hansen et al. 2008: https://onlinelibrary.wiley.com/doi/pdf/10./j.1558-5646.2008.00412.x. One trait evolves under Brownian motion, another trait follows it. Best, Brian ___ Brian O'Meara, http

Re: [R-sig-phylo] correlation of binary and multistate

ysbio/article/64/1/127/2847997. _______ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/> Associate Pr

Re: [R-sig-phylo] OU for non-ultrametric trees

relevant, the parameters you get from stretching also don't mean anything. [I imagine you're doing it well, just a teachable moment for new students on the list]. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially

Re: [R-sig-phylo] patristic distance doubts and meanings

, like those generated from modern high-throughput sequencing, like metabarcoding. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.in

Re: [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction

treats them as continuous. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://b

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

Brian ___ Brian O'Meara, http://brianomeara.info, especially Calendar <http://brianomeara.info/calendar.html>, CV <http://brianomeara.info/cv.html>, and Feedback <http://brianomeara.info/feedback.html> Professor, Dept. of Ecology & Evolut

Re: [R-sig-phylo] Phylogenetic varying slopes and intercepts model

Brian ___ Brian O'Meara, http://brianomeara.info, especially Calendar <http://brianomeara.info/calendar.html>, CV <http://brianomeara.info/cv.html>, and Feedback <http://brianomeara.info/feedback.html> Pro

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

___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/>

Re: [R-sig-phylo] ancestral state transitions clustered in time?

f many methods that look at rates, such as the ones here. Best, Brian _______ Brian O'Meara Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, U

Re: [R-sig-phylo] Alllowing and considering "missing data" as values for reconstruction of ancestral character states

ot;) seems unexpected to me. Best, Brian _______ Brian O'Meara Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville He/Him/His On Mon, Apr 1

Re: [R-sig-phylo] Alllowing and considering "missing data" as values for reconstruction of ancestral character states

eneral tips there. Slightly better style would be to preface most functions with the package name: use corHMM::rayDISC() rather than rayDISC -- this is becoming more expected in packages. Best, Brian ___ Brian O'Meara Professor,

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

Best, Brian ___ Brian O'Meara Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville He/Him/His On Fri, May 22, 2020 at 9:42 AM Karla Shikev wrote: