I just submitted a new version of phytools (phytools 0.4-31) to CRAN. Hopefully it will be accepted and post within 24 hrs.
Some updates in this version include the following:
1. An important bug fix in the phytools function
make.simmap for multi-state data.
2. A new version of the phytools 'robust' tree reader,
read.newick, that permits a root edge length.
3. New user controls for the function
phylo.to.map for projecting a phylogeny onto a geographic map (described here).
4. An update to the phytools function
locate.yeti permitting the unknown leaf to attach below the root node of the base tree.
5. A bug fix for the S3 plotting method for objects of class
"describe.simmap" (described here).
6. A bug fix for the phytools wrapper function
plotBranchbyTrait that corrects the orientation of labels on fan trees, among other things.
7. A new version of
threshBayes with an option to suppress printing the MCMC status to screen (which can be annoying for very long chains).
8. A bug fix in
read.simmap to address a problem in which trees could not be read from a text string (only from file).
drop.tip 'methods' for objects of class
"densityMap". This also permits the user to supply internal node values to
I have posted a source build to the phytools page. Hopefully it is also on CRAN soon.
That's it for now.