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

he the edge with low support. 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, 20

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

;))) } dev.off() Hopefully a few general 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 __

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,

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

the issues raised affect our interpretation of 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, De

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

digging. Best, 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/fe

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

ut it might be more complex. Best, 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>

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

.sq) and param.count is 2 (root state, though the MLE for this does not require optimization as there's an equation for it), so they should be comparable. Best, Brian _______ Brian O'Meara, http://brianomeara.info, especiall

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

ht_asym 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/

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

nomic data sets, 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 <h

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

software mistakenly 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/>,

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

tarting branch lengths don't mean something that's 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 ________

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

the covariance. 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

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

ate.tree, outline=FALSE, 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/ome

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

you find that 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'Me

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

eve bayou 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.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 seem to not quite be

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'

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,

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/omear

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

alf life: ", round(log(2)/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=poin

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

demic.oup.com/sysbio/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/feedbac

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

r phangorn, for example, assuming it actually works]. Best, Brian _______ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>

Re: [R-sig-phylo] chronoMPL/APE

L, or similar. Best, Brian ___ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomea

Re: [R-sig-phylo] A question about phylogenetic signal significance with 1000 trees

, or built in functions) choose the particular scaling to be appropriate for each tree, and so the distribution across them doesn't matter in that case. Best, Brian _______ Brian O'Meara, http://www.brianomeara.info, especiall

Re: [R-sig-phylo] Making ultrametric trees

biological results that are sensitive to branch lengths (and the degree to which methods are sensitive to branch length errors does vary by method) you might need to invest in the harder analyses. Best, Brian _______ Brian O'

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

et for something that matters, but it should make all this easier 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, htt

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

ink about ways to go from what 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

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/feedbac

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

all, and I 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://br

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 Prof

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

approaches, but I doubt 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.brianomear

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

nd macroevolutionary 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, 20

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

mp; FitzJohn, 2014: 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://nim

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

the moment. 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/ Calendar: http://www.brianomeara.info/calendars/omeara On Mon, Nov 3

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&

Re: [R-sig-phylo] using chronos() from the ape package for large bacterial phylogeny

Geiger has an interface to pathd8; it has the beginnings of interfaces to other programs, too, but I don't think they're finished yet. Best, Brian _______ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennes

Re: [R-sig-phylo] Dollo character using ace/make.simmap

rate from 0->1 and allow a higher 1->0 rate. If the clade starts in state 1, then treating it as irreversible (rate 0->1 fixed at 0) would be fine. Best, Brian _______ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U.

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

you think that's how speciation happens (i.e., a polymorphic species with 0&1 speciates by separating into a 0 monomorphic species and a 1 monomorphic species). Best, Brian _______ Brian O'Meara Assistant Professor Dept. of Ecology & Ev

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

can deal with uneven sampling that you specify; diversitree does have trait only models, but I'm not sure if they incorporate sampling frequency. Hope this helps. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionar

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/omear

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

d and fix 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/po

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] ancestor vs. change plots

different rates 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

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

swer you didn't like, 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

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

ual chances of red 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'M

Re: [R-sig-phylo] Phylogenetic analysis with sequencing error

ust remember to trim off the extra tip lengths for the last regime when presenting the final tree, and this should give you exactly what you want. Hope this helps, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology

Re: [R-sig-phylo] chronos nlminb error

ot;correlated", quiet = FALSE, calibration = makeChronosCalib(tree), control = chronos.control()) Sometimes the imported tree structure, while valid, can be an issue for ape and I find doing this reordering can fix weird errors. Best, Brian _______

Re: [R-sig-phylo] binary trait influencing diversification

The diversitree package has a simulator for this. 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

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

s 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

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/

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 coll

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

r). [1] http://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 Tennesse

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

matter for signal, though some biased 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 E

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

's updated 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 Stude

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 Biol

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

tps://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/R/OUwie.contour.R?revision=133&root=ouwie. Best, Brian _______ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Stude

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

ts 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 collab

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

can be hard to find (I think 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 ___

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

d to OUwie 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: Appli

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/ca

Re: [R-sig-phylo] Identical likelihood values for OU and EB models

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' web

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

[yes, self-promotion]. 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 w

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

org/) to have R 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 col

Re: [R-sig-phylo] Problem with fitContinuous function

can see problems this way. 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 NIMBi

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

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' web

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

No, it's just univariate (I was responding to your example about doing a single character). For multivariate OU, I think OUCH is the only game in town. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U

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

to do. 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 NIMBioS' website Cal

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, Knoxv

Re: [R-sig-phylo] using ace (ape) with missing data

esults are not affected by decisions about how to treat missing data. Best, Brian _______ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications du

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

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' we

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

tructions. I have code around to do 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

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

a prior on the root state 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 D

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

omeone else may know of other ways to attack this problem. Hope 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.

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

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

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

n(phy.a, list(phy.a, phy.b, phy.c), type="mean_brlen") Best, 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'Mear

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

, you 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

Re: [R-sig-phylo] variation in rates over time, unexpected message when using Brownie.lite

don't deal well with these). 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 wa

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

as et al. (2006) 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 Stude

[R-sig-phylo] R resource on cluster

ve.org/discover/discovery-environment [2]: https://pods.iplantcollaborative.org/wiki/display/DEmanual/Integrating+an+Application+into+the+Discovery+Environment [3]: http://barbbanbury.info ___________ Brian O'Meara Assistant Professor Dept. of Ecology & Ev

Re: [R-sig-phylo] diversitree with multicore

lization, too. It's especially good if you still think in terms of for loops (as I do, sadly, though I'm working on it). Brian _______ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http:

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

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

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

igating if actual conclusions depend on the results. 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 NIMBi

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

etter 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 w

Re: [R-sig-phylo] reading nexus file from treebase?

TITLE and LINK are used by Mesquite but not many other Nexus-reading programs (TITLE appears as a future reserved command name in the Maddison et al. (1997) nexus specification but I don't see LINK there). Brian ___ Brian O'Meara Assistant Professo

[R-sig-phylo] Make all trees

rees. Does anyone know where to find the more general function? I can imagine several ways to write such a function, but reuse is better than reinvention. Thanks, Brian _______ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of T

Re: [R-sig-phylo] when not to use an ultrametric tree?

is sort of simultaneous character analysis for discrete trait models but not continuous ones yet, but perhaps some other program can link continuous characters in this way (or someone wants to modify Brownie?). Brian _______ Brian O'Meara Assistant Professor D

Re: [R-sig-phylo] Ultrametricize?

Sorry for how this sounds, but using data is probably the best way if your end goal is to do phylogenetically-controlled analyses (rather than just the focused goal on minimizing branch length differences between the two trees): download sequences and use them to infer branch lengths, perhaps with

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

es in ape, Geiger, and other packages. 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: Chec

[R-sig-phylo] Chambers award

nnounced in May and the award will be given at the 2010 Joint Statistical Meetings. Chambers Software Award c/o Fei Chen Avaya Labs 233 Mt Airy Rd. Basking Ridge, NJ 07920 f...@avaya.com _______ Brian O'Meara Assistant Professor Dept. of Ecology & Ev

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

g > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due De

[R-sig-phylo] Phylogenetics task view

ckages that aren't in CRAN but are available can (and should) be described in a task view, but they can't be installed as part of the install.views() feature -- another incentive to put things on CRAN. Thanks, Brian ------ Brian O

Re: [R-sig-phylo] Difference in alpha value estimates between geiger and OUCH - data

fo/r-sig-phylo -- Carl Boettiger Population Biology, UC Davis http://two.ucdavis.edu/~cboettig [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ---

Re: [R-sig-phylo] Different estimates of alpha with geiger and OUCH

g 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. of Tennessee, Knoxville __

Re: [R-sig-phylo] Plot paleontological data with epoch names

__ 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 &

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 ) though note that the package itself is not all cleaned up into install.packages()-ready form. You could also

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

x.lim=38) #problem It's possible the solution to my original potting issue lies 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 -

Re: [R-sig-phylo] apTreeshape

_ 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. of Tennessee, Knoxville __

[R-sig-phylo] Phylogenetics task view

d. You can direct suggestions for improvements to me. Thanks to all who helped build it in the past and to Ben Bolker and Achim Zeileis for helping to get it on CRAN. Best, Brian ------ Brian O'Meara http://www.brianomeara.info Assistant Prof

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

http://ape.mpl.ird.fr/ ___ 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 &a

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 () has trees for many groups and also allows you to download aligned data to m

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