Julien- Does mvSHIFT account for the OU rescaling issue on non-ultrametric trees that Graham mentions? If so, how?
Cheers, -Dave On Mon, Jun 2, 2014 at 5:26 PM, Julien Clavel <julien.cla...@hotmail.fr> wrote: > Hi Jon, > > Take a look at the "mvSHIFT" function in mvMORPH. This is typically what you > are looking for and you can use it with non-ultrametric trees (it's maybe > faster than classic functions). > > Best, > > Julien > >> Date: Mon, 2 Jun 2014 14:55:06 -0500 >> From: mitchel...@uchicago.edu >> To: r-sig-phylo@r-project.org >> Subject: [R-sig-phylo] Early burst branch rescale >> >> Hello all, >> >> I'm trying to figure out how to rescale certain branches of a tree >> according to an early burst model. >> >> First I've generated a tree using TreeSim >> >> N <- 100 >> >> Nn <- N*2 -1 >> >> test <- sim.bd.taxa(N, 1, 1, 0.8, complete=FALSE) >> >> >> Then I 'paint' the branches depending on whether or not they occur in the >> first or second half of the clade's history: >> >> >> Root <-max(nodeHeights(test2)) >> >> Age <- 0.5*Root >> >> test2 <- make.era.map(test[[1]][[1]], c(0, Age)) >> >> >> Using rescale() from geiger, I can reformat the whole tree, and using >> sim.rates() from phytools, it's easy to simulate different sigmas. But what >> I'd like to do is also simulate different evolutionary modes (OU and EB) in >> the different regimes (like Graham's MEE paper). Is there a way to rescale >> the branches in one portion of the tree according to the OU alpha or EB r >> parameters? >> >> Thanks! >> -- Jon >> >> _____ >> >> Jonathan S. Mitchell >> http://home.uchicago.edu/~mitchelljs/ >> >> PhD Student >> Committee on Evolutionary Biology >> The University of Chicago >> 1025 57th Str, Culver Hall 402 >> Chicago, IL 60637 >> >> Geology Department >> The Field Museum of Natural History >> 1400 S. Lake Shore Dr. >> Chicago, IL 60605 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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/ > > [[alternative HTML version deleted]] > > _______________________________________________ > 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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
