Friday, July 10, 2015

New version of phytools (phytools 0.4-60) on CRAN

Yesterday I submitted a new version of phytools to CRAN (phytools_0.4-60), and this afternoon it was accepted & posted.

There are no major new methods to report in this version over the last CRAN release of phytools; however I have made a number of different updates to a variety of frequently (& infrequently) used functions. Among these:

  1. An update to plot.contMap to permit user control of the legend text.

  2. A bug fix in phenogram for when ftype="off" (i.e., the traitgram is being plotted without labels.

  3. A bug fix for ltt for an input tree with node labels.

  4. A long overdue update to the ancestral state reconstruction function rerootingMethod to permit trees with multifurcations.

  5. New S3 print & plot methods, and a new custom object class, for the phytools lineage-through-time function ltt (here).

  6. A minor bug fix in the phytools function writeAncestors.

Finally, 7. an update to ltt to permit the lineage-through-time plot to include an overlain phylogeny (1, 2).

This new package update was also necessited by changing CRAN policies which now require that all internally used functions from core R packages, such as graphics, utils, and methods also be imported into the namespace and specified in the DESCRIPTION file - so you can also see that on the phytools CRAN page.

That's all for now! Hopefully there will be more interesting updates to report for the next new CRAN version of phytools.

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