Saturday, September 29, 2012

New version of phytools on CRAN

I just submitted a new version of phytools (version 0.2-0) to CRAN. This is basically the same as the latest "non-CRAN" release (0.1-98) with a couple of minor changes and corrections in the manual pages and to the function fancyTree. However, there have been lots of new additions and changes to phytools since the last CRAN update, version 0.1-9. Here's a (probably non-comprehensive) sample:

1) A new function, threshBayes, to analyze the threshold model from quantitative genetics (described here and here).

2) A new function, bmPlot, for visualizing Brownian motion evolution (here) and evolution under the threshold model (here).

3) A bug fix in the important phytools function nodeHeights (here).

4) An update to the canonical correlation analysis function phyl.cca, as well as some other things (described here).

5) Renaming & movement of the likelihood function for joint Pagel's λ for multiple characters to the NAMESPACE (described, along with instructions for using this function - likMlambda - to perform joint estimation of Pagel's λ, here).

6) Minor update to phylogenetic principal components function, phyl.pca (here).

7) New version of fitDiversityModel with much improved likelihood estimation (described here).

8) New tree plotting method in the function fancyTree (here) along with various improvements thereof (here).

9) A number of changes to documentation and some minor fixes and updates to internal phytools functions.

The source build of phytools 0.2-0 is already available from CRAN (although will not yet have percolated through all mirrors), and from my phytools page. Obviously, it may take a few days for Mac OS and Windows binaries to be available.

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