Hi Liam, Thanks for the speedy reply. Looks like a neat function.
I've tried it out, and I get perfect results on ultrametric trees, but non-ultrametric give me a funny result, a big uptick in the ltt plot right at the present. I wonder if it's something to do with the dates on the tree I'm using, which go from +ve to -ve. Code to reproduce the result is below. Thanks Rob library(TreeSim) library(phytools) library(geiger) #simulate tree of 100 taxa with initial diversification followed by a period of B=D t1 <- sim.rateshift.taxa(100, 1, c(0.2, 0.2), c(0.2, 0.05), c(1,1), c(0, 20 ))[[1]] t1 #confirm number of extant taxa is 100 n.extant <- length(prune.extinct.taxa(t1)$tip.label) n.extant #do ltt plot without extinct taxa (works fine) p1 <- ltt(t1, log.lineages=FALSE, drop.extinct=TRUE) #do ltt plot with extinct taxa (looks odd) p2 <- ltt(t1, log.lineages=FALSE, drop.extinct=FALSE) #max times don't seem to correspond between the two plots. max(p1$times)==max(p2$times) On 11 August 2011 10:55, Liam J. Revell <liam.rev...@umb.edu> wrote: > This is implemented in my "phytools" package. This is not yet on CRAN, but > can be downloaded from http://anolis.oeb.harvard.edu/** > ~liam/R-phylogenetics/<http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/>. > The function is ltt(). It is slow, but seems to work. Please let me know > if you have success with this. > > - Liam > > -- > Liam J. Revell > University of Massachusetts Boston > web: > http://faculty.umb.edu/liam.**revell/<http://faculty.umb.edu/liam.revell/> > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > > On 8/10/2011 8:51 PM, Rob Lanfear wrote: > >> Hi All, >> >> I have a set of simulated birth-death trees, which include extinct and >> extant lineages. I'd like to see if my simulations are doing what I think >> they should be, by plotting out the number of lineages through time. >> >> Does anyone know of a method of doing this that incorporates extinct >> lineages, i.e. one where the number of lineages can decrease as well as >> increase through time. >> >> I can see how it could be done (I think...) by making an ordered data >> frame >> of node times (+1 lineage) and extinction events (-1 lineage), but it >> seems >> like somebody might already have done it. >> >> Cheers, >> >> Rob >> >> -- Rob Lanfear Postdoc, Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University Tel: +61 2 6125 7270 www.robertlanfear.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
