Thursday, February 7, 2013

New version of phytools (0.2-16)

I just posted a new, non-CRAN phytools version (0.2-16). There are not a huge number of updates in this version from the last non-CRAN phytools version (0.2-15), but the updates since the last CRAN release (2012-11-13) are considerable. I plan to submit a new version to CRAN soon. Here is a list of updates in this version relative to phytools 0.2-15:

1. An updated version of pgls.Ives that can (optionally) compute sampling variances and covariances for species means internally.

2. A new function, add.random, which can add new tips at random to a tree (and also assign branch lengths to keep an ultrametric tree ultrametric, which is neat).

3. A new utility function, orderMappedEdge, which sorts the column order of $mapped.edge in a "multiPhylo" set of phylogenies with mapped discrete traits.

Finally, 4. updates to anc.ML, ancThresh, anc.trend, and anc.Bayes, to return a sensible error if internal or terminal branches of zero length will cause analyses to fail. Note that fastAnc, because it uses contrasts to get the ML ancestral states, needs a fulling bifurcating tree - although it can also convert the tree internally and then backtranslate the node IDs.

I think that covers everything.

As usual, you can download this version here and install from source:
> install.packages("phytools_0.2-16.tar.gz",type="source", repos=NULL)
* installing *source* package 'phytools' ...
** R

* DONE (phytools)

Please let me know if you find any bugs!

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