Hi Jeremy, Emmanuel and I had a off-list conversation after that email, so there was follow-up, we just never told the list about it!
To my knowledge, the issue I was having where not all clades shared were being detected with prop.clades was unique to 3.0-1. For example, under my 3.0-6 install of ape, the code from my old email actually does show multiple shared clades with prop.clades. Here it is again with ape 3.0-6: library(ape) library(paleotree) set.seed(3) tree1<-rtree(30) tree2<-degradeTree(tree1,0.5) layout(matrix(1:2,,2));plot(tree1);plot(tree2) and.... > prop.clades(tree1,tree2) [1] 1 2 0 0 0 1 1 0 0 1 0 0 1 1 0 0 1 1 1 0 1 0 0 1 1 0 1 0 0 Now, for the sake of posterity, it turns out the '2' which threw me in that original email was a result of me not telling prop.clades that my trees were rooted (and Emmanuel has updated the man page so this is crystal clear): > prop.clades(tree1,tree2,rooted=TRUE) [1] 1 1 0 0 0 1 1 1 0 0 1 0 0 1 1 0 0 1 1 1 0 1 0 0 1 1 0 1 0 Jeremy, could you make some example data where prop.clades underestimates shared clades? Also, have you also tried applying reorder.phylo or collapse.singles to your trees before trying prop.clades? -Dave On Thu, Nov 8, 2012 at 2:04 PM, Jeremy Yoder <jbyo...@gmail.com> wrote: > All, > > I'm working on some analyses that require comparison of tree structures, > and I've bumped into the problem David Bapst posted about back in March: > http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01840.html - > briefly, prop.clades() is failing to count many clades that are in common. > There doesn't seem to be any followup to that post; has anyone made > progress figuring it out? > > I'm currently using ape 3.0-6 and R 2.15.1 on a MacBook running Mountain > Lion. > > thanks, > Jeremy > > ---- > Jeremy B. Yoder > Postdoctoral Associate > Department of Plant Biology > University of Minnesota > > www.jeremybyoder.com (http://www.jeremybyoder.com) > > jbyo...@gmail.com > > Sent with Sparrow (http://www.sparrowmailapp.com/?sig) > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages/paleotree/index.html <http://home.uchicago.edu/%7Edwbapst/> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
