Sunday, February 17, 2013

New version of phytools on CRAN (phytools 0.2-20)

A new version of phytools (phytools 0.2-20) is now on CRAN. Presently you can download the source code for this version from the phytools homepage or phytools CRAN page and install from source. Windows and Mac OS binaries should be built soon and eventually these will percolate through all the different CRAN mirrors.

Due to updates in a couple of different functions, phytools now depends on ape ≥ 3.0-7 (the latest version of ape as of the present date) and imports from phangorn ≥ 1.6-3.

Here's a brief list of some of the updates in phytools 0.2-20 relative to the last CRAN version (0.2-1):

1. A new function, splitplotTree, to plot a phylogeny in multiple columns or plotting windows.

2. A new function, bind.tip, for adding a single tip to the tree (1, 2).

3. A couple of critical bug fixes for phyl.RMA (1, 2).

4. A significant update to the function matchNodes which matches nodes between trees based either on the descendant tips from each node or on the distances from nodes to the tips in the tree.

5. A new utility function, applyBranchLengths, which applies the branch lengths from one tree to other topologically identical phylogenies.

6. New versions of ancThresh (e.g., here) and user control of phytools function plotThresh and threshDIC.

7. A new function, add.random, to add tips at random to a phylogeny.

8. An important update to pgls.Ives, to accept individual data, rather than just species means and standard errors.

9. A new function, orderMappedEdge, to reorder the "phylo" object mapped.edge in SIMMAP style trees.

10. A new version of the function, mrp.supertree, for MRP supertree estimation (1, 2).

11. Update to the function phylANOVA for phylogenetic ANOVA based on Garland et al. (1993).

12. A new version of fastAnc to compute the variances and 95% CIs on ancestral states.

13. A new function, getSisters, to get the node(s) or tip(s) that are sister to a focal node.

14. Minor updates to several functions including add.everywhere, allFurcTrees, anc.Bayes, anc.ML, anc.trend, ancThresh, brownie.lite, estDiversity, evol.rate.mcmc, evol.vcv, evolvcv.lite, exhaustiveMP, fancyTree, fitBayes, make.simmap, optim.phylo.ls, phyl.pairedttest, phylomorphospace, plotSimmap, reroot, sim.corrs, sim.history, sim.rates, and write.simmap.

15. Finally, as I mentioned before, a change in the dependency relationship with ape and phangorn. phytools now depends on ape ≥ 3.0-7 - but imports from phangorn (≥ 1.6-3).

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