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] 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] 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] 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:

[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] 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

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] 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] 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] 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] 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] 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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] [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] 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] 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] 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] 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] 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] 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] 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] 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] 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] Detecting non-Brownian trait evolution

You could look at OUCH, which implements Ornstein-Uhlenbeck models (Hansen, 1997; Butler & King, 2004), to compare the fit of OU models vs a single rate Brownian motion model as another way of testing for non-Brownian evolution. I cowrote a paper (O'Meara et al., 2006) that develops tests

Re: [R-sig-phylo] tree thievery

confusing. reading into excel: use "Data" menu to separate into columns Wish list for g3data: csv format output? series 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 NESCent Durham, NC http://www.brianomeara.info ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

[R-sig-phylo] R hackathon anniversary

aper to NESCent () to help with development, training, or other informatics needs. Ongoing submission (no deadlines). Everyone is welcome to participate. Feel free to respond to the list with proposals/requests/suggestions/etc. ____ Brian O'Me

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

he package for matrix comparisons, > matrix visualisation, tensor analysis, random number generators on > pedigrees/phylogenies + more. > > Thanks, > > Jarrod > > Jarrod Hadfield > Brian O'Meara NESCent Durham, NC http://www.brianomeara.in

Re: [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)

downloaded packages are in /private/tmp/RtmpMpRHQe/downloaded_packages [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailin

Re: [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)

R, 4) type "library (phylobase)", does everything work? Brian On Mar 12, 2009, at 5:54 PM, Peter Cowan wrote: On Mar 12, 2009, at 1:00 PM, Brian O'Meara wrote: Well, using 10.4.11 on an intel mac, with developer tools installed, running R 2.8.1, and got the error when trying

Re: [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)

t;, : > installation of package 'phylobase' had non-zero exit status > > However, I was able to follow most of the Brian's four steps to > remove phylobase and then re-install it but source compilation > failed. Can you guys tell what is wrong with compilation? is th

Re: [R-sig-phylo] DNA sequence management for phylogenetics in R

Christoph Heibl has some R code that calls mafft for alignment (which I currently like better than Clustal, btw) and others that can interact with a postgreSQL database for storing info [according to the software description -- I haven't tried this]. See

Re: [R-sig-phylo] size-free morphometrics in phylogenetic framework

Hi, Dan et al. I've been worried about this for PCA. Mesquite has an "evolutionary PCA" approach, but as far as I know, this hasn't been published anywhere. Assuming the method implemented in Mesquite is done properly (which I think rather likely), it'd be relatively simple to compare the e

Re: [R-sig-phylo] how to append multiple gene files

Mesquite can do this, though it's a bit manual (though Mesquite can be batched). I have a perl script that takes a set of nexus files (with each file having many taxa and one aligned gene) and concatenates them, including adding missing taxa and setting up character sets, so you could put 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

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

[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] 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] 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] 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

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] 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] 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 ---

[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] 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] 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] 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

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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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 ________

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