Hi Zach.
What is your objective here? reorder.phylo reorders the edges in the �phylo� object, but does not usually change the order in which the tips are plotted. For that, you should look at ape::rotate or phytools::rotateNodes (I believe), ape::ladderize, or the argument tips in phytools::plotTree. All the best, Liam -- Liam J. Revell, Associate Professor of Biology University of Massachussetts Boston email: liam.rev...@umb.edu web: http://faculty.umb.edu/liam.revell Sent from Outlook Mail for Windows 10 phone From: Zach Culumber<mailto:zculum...@gmail.com> Sent: Thursday, August 11, 2016 10:48 AM To: r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org> Subject: [R-sig-phylo] Unable to reorder any phylo object with reorder.phylo Hi everyone, I seem to have an issue where I cannot get any trees (real data or simulated trees) to reorder. I've tried a lot of different things including updating packages, restarting R, using a different computer. My real trees have 501 tips, but I'm having this issue even when I simulate trees with just 25 or 50 tips. Currently using R 3.3.1 in Rstudio and APE 3.5. I also came across the trick of using: phy <- read.tree(text=write.tree(phy)) but that didn't seem to work either. The structure of the my phylo objects (my real trees and simulated trees) are fine when passed through checkValidPhylo. Ultimately, if it were just one tree I would do it in an outside program and just import the reordered tree, but I'm wanting to apply a reordering function across a multiphylo object. However, I can't seem to get a single tree reordered! I'm pasting some code below which is pretty boiler plate but *should* I believe work, but doesn't work for me. If anyone has any thoughts or advice, I would appreciate it. Thank you! #Simulate a single tree to test the reorder function tree1<-pbtree(n=500,scale=10,nsim=1) plot(tree1) #Reorder with pruningwise tree2<-reorder.phylo(tree1, "pruningwise") plot(tree2) Zach -- Zachary W. Culumber Postdoctoral Research Associate Kansas State University Division of Biology http://www.zwcresearch.com Coordinator Centro de Investigaciones Cient�ficas de las Huastecas Aguazarca http://www.cichaz.org [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]]
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