This afternoon I submitted a new version of phytools to CRAN. Assuming it is accepted, the new version (phytools 0.4-45), which is already available from the phytools page, should percolate through all of the CRAN mirror repositories over the next few days.
This version does not feature any significant updates over the most recent non-CRAN phytools release (although I did do some updating of the manual pages this morning before submitting); however the last CRAN update was August 26th of last year (phytools 0.4-31) so there are many changes and updates to phytools since that release.
Some updates and additions include the following (and I can't guarantee that this list is comprehensive):
(2) A new function (
a phylogeny with a mapped discrete character.
(3) An update to the discrete character history simulating function,
sim.history, to handle
(4) A small update to the
user control of shading.
(5) Replacement of the redundant phytools function
repPhylo with a
for a very mysterious bug in
(not by coincidence - these two functions use the same internals).
(7) A wrapper function implementating Pagel's (1994) method to test for correlated evolution of two binary traits. (Not in phytools, but I posted code for simulating binary character correlated evolution here.)
(8) An update to
ML and REML estimation methods.
(9) User control of the vertical range of labels in
phenogram. (Turns out
(10) A fossil version of
locate.yeti, called, creatively,
(11) A new version of the phytools helper function
setMap that can
the color map of an object of class
(13) A new option in
plotSimmap (and thus
vertical spacing of tips in a right or left-facing square phylogram.
And, finally, (14) a
pbtree with user-supplied tip labels (& non-zero extinction).
Thanks for paying attention!