Hi Dave, Yes it does that because it use vcv matrix (with the Eq. 6 of Hansen 1997). Therefore this is the phylogenetic (cophenetic) distance between tips which is used.
Best, Julien > From: [email protected] > Date: Mon, 2 Jun 2014 19:54:17 -0600 > Subject: Re: [R-sig-phylo] Early burst branch rescale > To: [email protected] > CC: [email protected]; [email protected] > > 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 <[email protected]> > 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: [email protected] > >> To: [email protected] > >> 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 - [email protected] > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> Searchable archive at > >> http://www.mail-archive.com/[email protected]/ > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at http://www.mail-archive.com/[email protected]/ > > > > -- > 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 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
