Re: [R-sig-phylo] Comparing support values on different trees

2016-12-16 Thread Emmanuel Paradis
Hi Frank, It seems that you can use the (apparently not used a lot) option from makeNodeLabel(, method = "md5sum") which creates node labels with the MD5SUM algorithm using the tip labels descending from each node (considering the tree as rooted). The result is, for each node, a label that

Re: [R-sig-phylo] Comparing support values on different trees

2016-12-16 Thread Frank T Burbrink
Hi Everyone, Thank you Jacob, Keith and Emmanuel for your responses. What I am trying to do is a little different than what the solutions posted here would do. I am not important a distribution of trees, but rather a single tree with the support values already included. So imagine something

Re: [R-sig-phylo] Comparing support values on different trees

2016-12-14 Thread Emmanuel Paradis
Hi Jake, What you describe looks very musch like the Lento method implemented in the function lento() in phangorn. consensusNet(), also in phangorn, implements something similar: the consensus network. prop.part(), in ape, is the function behind the two previous ones. bitsplits() is more

Re: [R-sig-phylo] Comparing support values on different trees

2016-12-14 Thread Jacob Berv
To clarify - the idea here is that you are asking which clades appear in ’subordinate’ trees relative to clades that exist in a consensus tree, and then interrogating the support values of the shared clades which exist in the ’subordinate’ trees? So for example, clade A appears in consensus

Re: [R-sig-phylo] Comparing support values on different trees

2016-12-14 Thread Keith Barker
Frank: You can import all of the trees into one or more multiPhylo objects, then use the ape functions prop.part or prop.clades (depending on what you want to do) to summarize different subsets (e.g., from different analyses). Here is an example with simulated trees: x<-rmtree(50,100)