In advance of a
I'll be teaching next week at the
Universidad Nacional del Comahue in
(reputedly) beautiful Bariloche, Argentina, I will be trying to get a new
version of phytools on CRAN. This update will have version number
It has been over five months since I last submitted a phytools update to CRAN. Obviously, there have been a ton of updates in that time. Here are some:
- More user control of the
backbonePhyloto permit multiple clades to have the same label.
phylo.to.mapwhich helped enable this nice plot:
- A new phytools function for showing a barplot next to a plotted tree,
plotTree.barplot(1, 2, 3).
function, related to
plotTree.barplot, to plot a boxplot next to a phylogeny (
plotTree.boxplot). Also see this addition permitting the boxplot to be build using the ‘formula’ method.
- A simple
phyl.pcato permit more columns than rows in the input data matrix.
plot.cophyloto permit sigmoidal linking lines.
- New function to resolve a polytomous node in all possible ways. (Also here.)
- Function to reorder the daughter edges of a multifurcation in all possible ways.
- New option to rotate polytomies for co-phylogenetic plotting using the algorithm developed for [10.] (here).
- Speed up & fixes for
option to get the variance and confidence intervals for reconstructed
tip states obtained using
- New function to
the likelihood surface for the phytools function
- Update to the function
add.color.barto permit the gradient color legend to be plotted vertically as well as horizontally.
- Additional user
control of the S3
plotmethod for objects of class
- Updates to tip label plotting and a new S3
- A new phytools function to find all possible node rotations of all nodes in a tree.
- A new
search for the
cophylofunction for co-phylogenetic plotting.
- Some updates to
fitMkto permit more user control of optimization.
- A small
to pass optional arguments to
- A fun
optimization method for
cophylo. The animation, shown below, shows the tree traversal and the node rotations of the tree gradually being improved by the algorithm:
- A very simple new cospeciation test in phytools.
- A function to compute a modified version of Grafen’s edge lengths.
- A cool S3
densitymethod for objects of class
- Some new
and user-control of phylogenetic scattergram plotting using
to permit more user control of line end types in
- An extremely
bd) to pull birth & death (species & extinction) rates from an object of class
"birthdeath"computed by ape.
- A simple new
- And, finally, a bunch of other miscellaneous updates to address issues raised when updating ape & phangorn.
I know this isn't comprehensive, but it is a survey reflecting the wide range of updates & changes to the package. Of course, now that phytools is on GitHub, it's super easy to track all the committed changes the package has seen.
I'll post again when the updated phytools makes it on CRAN!