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]/
