That all sounds great as gravy to me, Emmanuel. Thanks for clarifying the help file. -Cave
On Wed, Jan 22, 2014 at 4:08 AM, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > Hi David, > > You are right about this help page which is not so accurrate. I have > modified it with: > > "The test differs slightly whether the tree is rooted or not. An > urooted tree is considered binary if all its nodes are of degree three > (i.e., three edges connect to each node). A rooted tree is considered > binary if all nodes (including the root node) have exactly two > descendant nodes, so that they are of degree three expect the root > which is of degree 2." > > About the concept of rooted vs. unrooted, it is not so different from the > one in Newick. Consider the tree: > > (A,B,C); > > is it an unrooted (binary) tree, or a rooted tree with a basal trifurcation? > The presence of a root edge helps to solve this ambiguity, so: > > (A,B,C):0; > > is a (non-binary) rooted tree (note that both trees are graphically > identical). Ape considers the first tree as unrooted because it is the kind > of trees produced by many functions such as nj, bionj, etc. > > Best, > > Emmanuel > > Le 16/01/2014 17:32, David Bapst a écrit : > >> Liam and to those who responded privately, >> >> Yes, I understand that's the general reasoning for why ape refers to >> trees with a polytomous root as 'unrooted'. >> >> But if a tree with a basal trichotomy is an acceptable binary tree, >> this doesn't jive with the help description for is.binary.tree in ape. >> The references to 'two descendant nodes' is the help file's >> terminology, after all. In particular, it doesn't match the text about >> binary trees having 2Ntip-2 edges; that is only true for 'rooted' >> binary trees. >> >> I also don't think every instance of a polytomy existing at the root >> reflects a user who necessarily realizes such topologies are treated >> as 'unrooted'; after all, a user might have use cases where a polytomy >> at the root actually represents a real multifurcating branching event. >> Although I realize this has never fully agreed with ape's concept of >> rooted and unrooted, I know I generally input trees in R with >> polytomous roots because there's some uncertainty in the proper >> outgroup, or the outgroup got dropped between inference and analysis. >> Either way, the tree is rooted and has directionality, it just doesn't >> have a fully resolved root. There's probably even better examples of >> use cases involving polytomous roots that just aren't occurring to me >> right now. >> >> Users may also not be immediately familiar with the 'rooted' and >> 'unrooted' concepts in ape as related to the presence of polytomies at >> the root node; I know I wasn't familiar with this concept when I first >> started working with phylogenies in R (although I admit I did know by >> the time I used is.binary.tree in my code). >> >> So, I think some clarification might be needed about the application >> of this function. >> >> Cheers, >> -Dave >> >> On Wed, Jan 15, 2014 at 8:03 PM, Liam J. Revell <liam.rev...@umb.edu> >> wrote: >>> >>> Hi David. >>> >>> In an unrooted, fully dichotomous tree each internal node is attached to >>> three & exactly three nodes (some of which are tips). (In a rooted binary >>> tree one additional internal node exists, the root, which is attached to >>> only two nodes.) Ancestor & descendant have no meaning until the tree is >>> rooted. The fact that an unrooted tree stored as an object of class >>> "phylo" >>> has one node with three 'descendants' (these aren't actually all >>> descendants, as the tree is unrooted) is just an artifact of the way the >>> object is stored in memory & thus is.binary.tree is behaving correctly. >>> >>> All the best, Liam >>> >>> Liam J. Revell, Assistant Professor of Biology >>> University of Massachusetts Boston >>> web: http://faculty.umb.edu/liam.revell/ >>> email: liam.rev...@umb.edu >>> blog: http://blog.phytools.org >>> >>> >>> On 1/15/2014 3:34 PM, David Bapst wrote: >>>> >>>> >>>> Hi Emmanuel and the rest of the list, >>>> >>>> In some code, I use the ape function is.binary.tree to test if a >>>> phylogeny is fully dichotomous. However, some recent analyses have >>>> made me wonder if this wasn't the right choice. I'm not sure if the >>>> following is a bug report me or me not understand the reasoning of a >>>> function in ape. >>>> >>>> You see, I had an 'unrooted' (in ape terminology) tree with a basal >>>> trichotomy. I wouldn't consider such a tree to be fully dichotomous, >>>> but is.binary.tree says such a tree is in fact binary (i.e. returns >>>> TRUE). It appears to be limited to just trees with basal trichotomies. >>>> If the root is an even larger polytomy (more than three descendant >>>> nodes), is.binary.tree returns FALSE. >>>> >>>> I was a bit surprised, as the function description says "This function >>>> tests whether a phylogenetic tree is binary, i.e. whether every node >>>> (including the root node) has exactly two descendant nodes." This >>>> would make me think it also tests if the root has two descendant >>>> nodes, but that doesn't seem to be the case, unless an unrooted tree >>>> with three lineages is (for some reason I'm unaware of) considered to >>>> have two descendant nodes. >>>> >>>> There's also some stuff in ?is.binary.tree about fully dichotomous >>>> trees having 2Ntip-2 edges, which is only true if the root is also >>>> dichotomous (and thus the tree is 'rooted'). It isn't true for taxa >>>> with a basal trichotomy. >>>> >>>> Here's some code. I got the same results with both ape v3.0-11 and the >>>> v3.1 that Emmanuel had sent out two weeks ago. >>>> >>>> library(ape) >>>> >>>> tree<-rtree(10) >>>> #collapse root >>>> tree$edge.length[which(tree$edge[,1]==11)[1]]<-0 >>>> tree1<-di2multi(tree) >>>> is.binary.tree(tree1) >>>> is.rooted(tree1) >>>> >>>> tree<-stree(3) >>>> is.binary.tree(tree) >>>> is.rooted(tree) >>>> >>>> tree<-stree(4) >>>> is.binary.tree(tree) >>>> is.rooted(tree) >>>> >>>> Is.rooted correctly returns FALSE, so does that mean best practice to >>>> get a tree where every node has two descendant nodes would be use >>>> is.binary.tree() & is.rooted()? >>>> >>>> Curious on your thoughts on this and the intent of is.binary.tree. >>>> >>>> -Dave >>>> >>> >> >> >> > -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
