David Bapst asked: > > I was interested if anyone was familiar with R code that can estimate an > extended majority consensus tree (referred to as an 'allcompat' tree by the > sumt command in MrBayes)? This is a fully bifurcating summary of a tree > posterior, where each clade is maximally resolved by the split that is most > abundant in the considered post-burn-in posterior (i.e., that split which > has the plurality, if not the majority - the highest posterior probability > of any other competing, conflicting splits recovered within the posterior. > So, I guess one could also call these plurality consensus trees...).
You can also get the Extended Majority Rule consensus tree from the Rconsense function in Liam Revell's package Rphylip, which is calls programs from my PHYLIP package. Consense in PHYLIP does output, in addition to the consensus tree itself, a list of partitions found in the input trees, and the frequency of each. Rconsense may be able to do that too. Speaking as the one who defined the EMR method, I need to make a warning: EMR makes a tree by ordering the partitions (splits) in order of their frequency. To make Margush and McMorris's Majority Rule consensus tree one simply goes down this list and takes all the partitions that occur more than 50% of the time. EMR continues further, in order to resolve the tree fully. It keep accepting partitions as long as they don't conflict with anything already accepted. But this means that two partitions could be found (say) 45% of the time each. They could both be compatible with the partitions in the majority-rule tree, but in conflict with each other. Which then gets included then depends only on which one is encountered first as one goes down the list of most-frequent partitions. And that will just be a matter of things like the order in which the tree containing them occurs among the input trees. That is one of the limitations of the EMR method. Note also that EMR is subtly different from finding the largest set of split (partitions) that are all mutually compatible. That will often be the same, but not always. The latter is called the Nelson Consensus Tree. Joe ---- Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA _______________________________________________ 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/
