Hi Jon, So there are are a few ways I can imagine doing this. One thing you should probably not do though is rescale the branches of the tree directly, at least in the case of OU, as this leads to incorrect covariances for pairs of taxa where one or either does not survive to the present day (see this in press note: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12201/abstract), as I suspect you have in your tree.
Probably the most appropriate way is therefore to 1) split the VCV into one or more matrices describing the variances and covariances over the intervals that youre interested in; 2) transform the matrices according the model and associated parameters you want over that interval, 3) stick them back together, and 4) draw your data directly from a multivariate normal distribution using the transformed covariance matrix. Ill send you some code off list to do that (its also in the corrected dryad pack accompanying the note above) Graham ------------------------------------------------------------ Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 [email protected]<mailto:[email protected]> www.fourdimensionalbiology.com<http://www.fourdimensionalbiology.com> On Jun 2, 2014, at 3:55 PM, Jonathan Mitchell <[email protected]<mailto:[email protected]>> wrote: 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]]
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