Tuesday, August 26, 2014

New version of phytools submitted to CRAN

I just submitted a new version of phytools (phytools 0.4-31) to CRAN. Hopefully it will be accepted and post within 24 hrs.

Some updates in this version include the following:

1. An important bug fix in the phytools function make.simmap for multi-state data.

2. A new version of the phytools 'robust' tree reader, read.newick, that permits a root edge length.

3. New user controls for the function phylo.to.map for projecting a phylogeny onto a geographic map (described here).

4. An update to the phytools function locate.yeti permitting the unknown leaf to attach below the root node of the base tree.

5. A bug fix for the S3 plotting method for objects of class "describe.simmap" (described here).

6. A bug fix for the phytools wrapper function plotBranchbyTrait that corrects the orientation of labels on fan trees, among other things.

7. A new version of threshBayes with an option to suppress printing the MCMC status to screen (which can be annoying for very long chains).

8. A bug fix in read.simmap to address a problem in which trees could not be read from a text string (only from file).

Finally, 9. drop.tip 'methods' for objects of class "contMap" and "densityMap". This also permits the user to supply internal node values to contMap.

I have posted a source build to the phytools page. Hopefully it is also on CRAN soon.

That's it for now.

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