Thank you Emmanuel! On close reading of the help files:
-------------------------------------- nl<-prop.clades(conTR, tr)/length(tr) plot(conTR) nodelabels(nl) --------------------------------------- Seems to work perfectly. [[elided Hotmail spam]] Cheers Sam ---------------------------------------- > Date: Mon, 18 May 2009 10:22:40 +0200 > From: emmanuel.para...@mpl.ird.fr > To: s_d_j_br...@hotmail.com > CC: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Consensus frequencies > > Hi Sam, > > Have a look at the function prop.part: it is the working function of > consensus and other similar functions. > > EP > > Sam Brown a écrit : >> >> Hello one and all >> >> I'm wondering if there is any way of obtaining the consensus >> frequencies of nodes in majority-rule consensus trees where p=0.5. >> >> i.e. given: >> >> >> t1 <- "((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7))));" >> t2 <- "((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7))));" >> t3 <- "((t4,t8),((t10,((t2,t5),t3)),((t6,t9),(t1,t7))));" >> t4 <- "((t2,t10),((t5,((t4,t3),t8)),((t6,t9),(t1,t7))));" >> t5 <- "((t10,t5),((t8,((t2,t4),t3)),((t6,t9),(t1,t7))));" >> t6 <- "((t4,t10),((t8,((t3,t5),t2)),((t6,t9),(t1,t7))));" >> t7 <- "((t4,t3),((t5,((t2,t10),t8)),((t6,t9),(t1,t7))));" >> t8 <- "((t4,t2),((t10,((t8,t5),t3)),((t6,t9),(t1,t7))));" >> t9 <- "((t4,t3),((t8,((t10,t5),t2)),((t6,t9),(t1,t7))));" >> t10 <- "((t10,t8),((t4,((t2,t3),t5)),((t6,t9),(t1,t7))));" >> >> tr<-read.tree(text=c(t1,t2,t3,t4,t5,t6,t7,t8,t9,t10)) >> >> conTR<-consensus(tr, p=0.5) >> plot(conTR) >> >> >> >> The node (t3,t2,t5) will have a consensus frequency of 0.5 (50%) and >> the three nodes ((t6,t9),(t1,t7)) will each have a frequency of 1 >> (100%). >> >> Are there any quick ways of getting this information? >> >> Thanks for any help/pointers >> >> Sam >> >> >> >> _________________________________________________________________ >> [[elided Hotmail spam]] >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _________________________________________________________________ enger! _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
