Saturday, June 29, 2013

phytools page down again - new version of phytools submitted to CRAN

The phytools page is having problems again. This is a UMass-Boston server-wide issue, so there is not much I can do about it unfortunately (aside from complain to the system administrator). To make all the recent updates to the phytools package available to all users, however, I have just submitted a new version of phytools to CRAN. Hopefully this version is accepted and made available via the CRAN mirrors as well as in binary form soon.

Some updates in this version over the previous CRAN release (phytools 0.2-80) include the following:

1. A new function to add a legend to a plotted stochastic map tree (add.simmap.legend).

2. A new version of plotSimmap that sets the environmental variable "lastplot.phylo" to be compatible with ape functions nodelabels, tiplabels, and edgelabels.

3. A new version of findMRCA that can also (optionally) return the height above the root of the MRCA of a pair of taxa.

4. A robust Newick tree reader that can handle singleton nodes, if present.

5. A bug fix in brownieREML.

6. A new function (collapse.to.star) that collapses specified subtrees into a star tree, while retaining the same total height above the root for each tip.

7. New versions of the phytools 3D functions phylomorphospace3d and fancyTree(...,type="traitgram3d") that work a little better with the functions of rgl (described here).

8. User control of tip & internal node sizes in phylomorphospace..

9. A hacky work-around fix for the problem of attaching a new tip separated from an existing tip by zero lenth using bind.tip.

10. Finally, today, a fix to the broken function evol.vcv, which is the function implementing the method of Revell & Collar (2009).

Hopefully this new phytools update is accepted and posted to CRAN soon.

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