I just posted a new minor version of 'phytools' (v0.2-03). This package version has the new function densityMap, for visualizing the posterior density from the stochastic mapping of a binary character on the trees; multi.mantel for partial Mantel tests; and the new major function for ancestral character estimation under the threshold model, ancThresh (1, 2, 3, 4). The function densityMap can also now be called from with fancyTree; and I fixed a couple of bugs in densityMap from the first version - particularly pertaining to the plotted legend, which wasn't showing up correctly. Finally, the package also includes a number of significant updates to other functions as well. Please check it out.
To install, just do the usual - first download the package source here, and then type: