Wednesday, February 4, 2015

New phytools version (phytools 0.4-45) submitted to CRAN

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):

(1) A faster version of the robust Newick tree reader read.newick (1, 2).

(2) A new function (ladderize.simmap) to ladderize a phylogeny with a mapped discrete character.

(3) An update to the discrete character history simulating function, sim.history, to handle errors more sensibly.

(4) A small update to the fancyTree method "phenogram95" to permit user control of shading.

(5) Replacement of the redundant phytools function repPhylo with a valid alias.

(6) A fix for a very mysterious bug in plot.contMap and plot.densityMap (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 locate.yeti implementing exact ML and REML estimation methods.

(9) User control of the vertical range of labels in phenogram. (Turns out this isn't particularly useful.)

(10) A fossil version of locate.yeti, called, creatively, locate.fossil.

(11) A new version of the phytools helper function setMap that can automatically invert the color map of an object of class "contMap" or "densityMap".

(12) A new function add.arrow that will add an arbitarily colored arrow to a radial or horizontal phylogram.

(13) A new option in plotSimmap (and thus plotTree) that permits arbitrary vertical spacing of tips in a right or left-facing square phylogram.

And, finally, (14) a bug fix for pbtree with user-supplied tip labels (& non-zero extinction).

As noted earlier, phytools 0.4-45 is already available from the phytools webpage, but, if all goes smoothly, should also be available from CRAN in the not-too-distant future.

Thanks for paying attention!

1 comment:

  1. Thanks for the update!
    I've tracked down some good datasets for case studies using locate.yeti. I've been excited about the idea since Seville. I'll let you know if I find anything cool.
    Cheers

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