Friday, June 24, 2016

New version of phytools (0.5-38) on CRAN

There is a new version of phytools (0.5-38) on CRAN in advance of the workshop I will teach this coming week in San Juan, Puerto Rico with Mike Alfaro, Ricardo Betancur, and Luke Harmon.

Here are some of the updates for this version:

  1. A simple function (matchLabels) to match labels between trees.

  2. A new function (consensus.edges) containing various methods to compute the consensus edge lengths from a set of trees.

  3. Fixes to the functions dotTree and fitPagel (here). (Also here: 1, 2.)

  4. An update to evol.vcv to fit a one matrix only model. (I also subsequently pushed an update to allow it work for only one trait too.)

  5. New S3 method updates for object classes "simmap" and "multiSimmap" and new function mapped.states (here).

  6. More important fixes to dotTree for trees containing few taxa.

  7. Some internal (but important) ways in which the way phytools plots left-facing trees. (Also here.)

  8. New function, averageTree for computing the 'average' phylogeny in a set, by some criteria (1, 2, 3, 4).

  9. Separate user control of left- and right-facing tree font sizes in plot.cophylo (here).

  10. Update to cophylo to permit links in assoc for taxa not found in the trees (here).

  11. Simple as.phylo method for objects of class "simmap" and "multiSimmap" (here).

  12. New options for setting the root state in sim.history.

  13. A version of bind.tree for objects of class "simmap" (also here).

  14. Important updates to fitPagel to permit different dependency relationships between traits and different models of evolution.

  15. New options for user control in dotTree (here).

  16. A new S3 plot method for objects of class "fitPagel" (1, 2).

  17. S3 plotting method for discrete character models fit using fitMk or fitDiscrete in the geiger package (1, 2, 3).

  18. Important updates to the method (here).

  19. Update to function (multiC) for computing multiple phylogenetic VCV matrices depending on the state of a mapped trait (here).

  20. Important bug fix for the function contMap.

  21. Update to roundPhylogram to permit different line edges and types.

  22. Finally, a new interactive version of phylo.toBackbone to permit a backbone tree with subtrees plotted as triangles to be created interactively, rather than via a static translation table (here).

These updates are already on CRAN - but it will probably take a couple of days for binaries to be built and percolate through the mirror repositories. In the meantime, as always, phytools can be installed from GitHub. Enjoy!

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