Saturday, April 20, 2013

New major version of phytools 0.2-50

I just submitted a new major phytools release to CRAN. If accepted, it should be posted to the phytools CRAN page within a couple of days & then gradually percolate through all the CRAN mirrors.

Here's a sample of some of the updates relative to the last major release of phytools:

1. A new version of plotSimmap that uses colors from palette() if none are provided.

2. Two new functions to compute & use the Strahler numbers of trees & nodes (1, 2).

3. A new version of estDiversity, with a new method that uses stochastic character mapping (1, 2).

4. A couple of fixes & updates to make.simmap (e.g., 1, 2).

5. A new, totally rewritten version of reroot, a function to re-root a tree along any internal or terminal edge.

6. A new function ltt95 to compute the (1-α)% confidence interval around a lineage-through-time plot from a set of trees.

7. A bunch of cool updates to pbtree including: simulating in discrete or continuous-time; simulating with taxa or time stops or both (by two different methods: 1, 2); and simulating deaths as well as births.

8. An updated version of anc.ML, that should work much better for large trees.

9. A new method for conducting marginal ancestral state reconstruction of discrete characters when tip values are uncertain.

It may be a few days before this update is available on CRAN, but interested users can download & install from source from the phytools page. Please let me know of any bugs or issues!

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