Re: [R-sig-phylo] TreeBASE Query Issue

Hi Skylar, Apologies for the problems, I'm the maintainer of the treebase R package. The API maintained by the TreeBase team appears to have started returning only empty results now, and as that is not the R side I will have to follow up with the TreeBase maintainers and figure out if the API

Re: [R-sig-phylo] fitting multiple OU optima

them using AIC. Cheers, Santiago ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Carl Boettiger UC Santa

Re: [R-sig-phylo] p-values and fitContinous from geiger

-project.org/http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Carl Boettiger UC Santa Cruz http://carlboettiger.info/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-phylo] LL ratio test

://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-phylo] LL ratio test

]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted

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

[[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version

Re: [R-sig-phylo] convergence issues with hansen model

       [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ ___ R-sig

Re: [R-sig-phylo] very large sigma squared values

-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r

Re: [R-sig-phylo] very large sigma squared values

Title pascalti...@gmail.com wrote: Thanks for the quick response! At the suggestion of another reader, I made my tree ultrametric and this greatly improved the parameter estimates. Using the ultrametric tree, I did the quick calculation for one variable that Carl Boettiger suggested, and found

Re: [R-sig-phylo] fitContinuous in geiger

-- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[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] LASER profile likelihood by sliding window

and Systematics Group Department of Botany Rhodes University Grahamstown 6140 SOUTH AFRICA Tel: + 27 (0)76 419 6656 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC

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

at some point. It does seem to be a Linux specific problem though, and I'm not sure what's going on. Cheers Matthew On 11-05-18 09:42 AM, Carl Boettiger wrote: Hi List, On one of my computers I get anomalous results from various birth-death simulations, which behave fine on my other

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

() with a tol option set to 1e-8 by default. I wonder whether it gives different outputs than geiger's function. Best, Emmanuel -Original Message- From: Carl Boettiger cboet...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Wed, 18 May 2011 09:08:23 To: Matthew Vavrekmatt

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

-- Tanja Stadler (nee Gernhard) ETH Zürich Institute of Integrative Biology Universitätsstrasse 16 8092 Zürich eMail: tanja.stad...@env.ethz.chmailto:tanja.stad...@env.ethz.ch Phone: +41 44 632 45 48 Office: CHN H76.1 http://www.tb.ethz.ch/people/tstadler -- Carl Boettiger UC Davis

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

? On Wed, May 18, 2011 at 3:59 PM, Carl Boettiger cboet...@gmail.comwrote: Hi Tanja,list Yes, everything is going extinct, but as you say, that shouldn't happen when mu = 0. sim.bd.age(age=2,numbsim=3,lambda=2,mu=0,frac,mrca=FALSE,complete=FALSE) [[1]] [1] 0 [[2]] [1] 0 [[3]] [1] 0

Re: [R-sig-phylo] summarising a frequentist test over a Bayesian sample of trees

-- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[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] erroneous results with rTraitCont simulations of the OU process

branch of the tree at your will, and you can output the ancestral values of each run. Carl Boettiger wrote on 05/03/2011 02:15: Dear Emmanuel, List, Thank you for the reply, I hadn't realized that rTraitCont simulates the trait evolution numerically from the SDE. I believe it would be more

[R-sig-phylo] erroneous results with rTraitCont simulations of the OU process

. Performing simulations of the same model on the same tree in ouch does not give this error. Perhaps I've missed something in my call to rTraitCont? Thanks for your time and advice! Carl -- Carl Boettiger UC Davis http://www.carlboettiger.info

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

-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r

Re: [R-sig-phylo] geiger: applying fitDiscrete to multiple variables over a tree sample

-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger Population Biology, UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https

Re: [R-sig-phylo] geiger: applying fitDiscrete to multiple variables over a tree sample

h h taxon4 g h g NA taxon5 i j NAa ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl Boettiger Population Biology, UC Davis http

Re: [R-sig-phylo] geiger: applying fitDiscrete to multiple variables over a tree sample

Database http://www.bu.edu/phylogeny/ Evolutionary Architecture of Reproduction website http://www.dur.ac.uk/reproductionproject/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl

Re: [R-sig-phylo] Problems with fitDiscrete

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

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

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

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

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

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

for Brownian motion in ouch/geiger/ape algorithms for fitting a Brownian motion model? Perhaps I've overlooked something? -Carl -- Carl Boettiger Population Biology, UC Davis http://two.ucdavis.edu/~cboettig [[alternative HTML version deleted]] ___ R

[R-sig-phylo] unexpected behavior in ouch

. Cheers, Carl -- 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] Use of OUCH package

): http://www.iee.uu.se/zooekol/default.php?type=personalpagelang=enid=146        [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Carl