I'm submitting a new version of phytools to CRAN. The last update went up around the end of March, so needless to say the package has seen many fixes, modifications, and even a number of new functions since that time. Here is a non-comprehensive list - but all changes to phytools can also be tracked on its GitHub page.
New function to add tip labels to the tree with linking lines (here).
Update to the function
treeSliceto crop the tipward end of a phylogeny (here).
A fix to the S3
"phyl.RMA"class objects (here).
A significant extension of the S3
"multiSimmap"class objects (here).
Fix & extension of the S3 method
plot.changesMapto visualize all the changes from a set of stochastic character map trees (here).
plot.cophylofor co-phylogenetic plotting to permit different edge colors to be used in one or the other plotted trees (here).
A completely new method,
ratebytree, for comparing the evolutionary rate for a continuous character between two or more trees (here).
A complete re-write of phytools
densityTreefunction for plotting a sample of trees, including with mapped discrete characters (here).
An update to the
plotmethod for the
"multiSimmap"object classes to permit slanted phylograms (here).
A completely new function to compare the node heights of two plotted chronograms (aka. time-trees; here).
A simple new function,
geo.legend, to overlay a geological timescale onto a plotted tree (here).
A general function and some associated methods for expanding or contracting the tip spacing of certain subtrees on a plotted phylogeny (here).
A small bug fix in the popular function
fastBMfor non 'cladewise' ordered trees (here).
Another bug fix for
read.newickfor the cases in which some but not all internal nodes are labeled (here).
New user control over the color & width of the plotted arcs in
The CRAN submission has version number 0.6-20. Hopefully it is accepted. I'll keep you posted! It is already available via GitHub.