Hmm. I should try solutions before I post them. You need to make sure that each tree in the list is of class phylo too. This works:
phylist<-read.tree(text="((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);") newnames<-c("G","H","I","J","K") newlist <- lapply(phylist, function(z) { z$tip.label <- c("G","H","I","J","K") class(z) <- "phylo" z }) class(newlist) <- "multiPhylo" write.tree(newlist,file="newlist") On Mon, 2008-09-01 at 10:55 +1000, Simon Blomberg wrote: > Try > > class(newlist) <- "multiPhylo" > > Then use write.tree. > > Cheers, > > Simon. > > On Sun, 2008-08-31 at 20:39 -0400, [EMAIL PROTECTED] wrote: > > Hi all, > > I have hit an obstacle and I hope someone will know a quick fix. I > > want to read > > a list of trees, do something to those trees and then write them to a > > file. The list is seen as multiPhylo until I apply some function then > > it becomes a > > list that I cannot write to a file with write.tree. I put an example below, > > where I read in two trees, and then use a function to change the tip names > > and > > then try to write the trees to a file. > > Thanks in advance for your help! > > Stacey > > > > > phylist<-read.tree(text="((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00); > > > > > > ((((A:0.21,B:0.21):0.28,C:0.49):0.13,D:0.62):0.38,E:1.00);") > > > class(phylist) > > [1] "multiPhylo" > > > newnames<-c("G","H","I","J","K") > > > newlist <- lapply(phylist, > > + function(z) { > > + z$tip.label <- c("G","H","I","J","K") > > + z > > + }) > > > write.tree(newlist,file="newlist") > > Error in write.tree(newlist, file = "newlist") : > > object "phy" is not of class "phylo" > > > > (and yes, write.tree did work on the multiphylo object before I did the > > function) > > > > _______________________________________________ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo