Saturday, July 26, 2014

Bug fix for S3 plotting method for objects of class "describe.simmap"

In recent phytools versions the phytools function describe.simmap returns an object of class "describe.simmap" which, if plotted, shows a phylogeny with posterior probabilities from stochastic mapping shown as pie charts at each node and tip of the tree. Unfortunately, when I switched the internal tree plotting function from ape's plot.phylo to plotTree in phytools, I made a mistake in setting the automatic offset of tip labels such that labels are frequently plotted outside the plotting window. This bug was reported to me today by a colleague and I just posted a new version of phytools with the bug in this plotting method fixed. This phytools version (>=0.4-26) can be downloaded from the phytools page and installed from source. Obviously, this fix will also be in subsequent CRAN releases of the phytools package.

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