Wednesday, July 26, 2017

New phytools version submitted to CRAN

I'm submitting a new version of phytools to CRAN. The last update went up around the end of March, so needless to say the package has seen many fixes, modifications, and even a number of new functions since that time. Here is a non-comprehensive list - but all changes to phytools can also be tracked on its GitHub page.

  1. New function to add tip labels to the tree with linking lines (here).

  2. Update to the function treeSlice to crop the tipward end of a phylogeny (here).

  3. New S3 print method for evolvcv.lite (here).

  4. A fix to the S3 plot method for "phyl.RMA" class objects (here).

  5. A significant extension of the S3 density method for "multiSimmap" class objects (here).

  6. Fix & extension of the S3 method plot.changesMap to visualize all the changes from a set of stochastic character map trees (here).

  7. Update to plot.cophylo for co-phylogenetic plotting to permit different edge colors to be used in one or the other plotted trees (here).

  8. A completely new method, ratebytree, for comparing the evolutionary rate for a continuous character between two or more trees (here).

  9. A complete re-write of phytools densityTree function for plotting a sample of trees, including with mapped discrete characters (here).

  10. An update to the plot method for the "simmap" and "multiSimmap" object classes to permit slanted phylograms (here).

  11. A completely new function to compare the node heights of two plotted chronograms (aka. time-trees; here).

  12. A simple new function, geo.legend, to overlay a geological timescale onto a plotted tree (here).

  13. A general function and some associated methods for expanding or contracting the tip spacing of certain subtrees on a plotted phylogeny (here).

  14. A small bug fix in the popular function fastBM for non 'cladewise' ordered trees (here).

  15. Another bug fix for read.newick for the cases in which some but not all internal nodes are labeled (here).

  16. New user control over the color & width of the plotted arcs in arc.cladelabels (here).

The CRAN submission has version number 0.6-20. Hopefully it is accepted. I'll keep you posted! It is already available via GitHub.


  1. Just wondering in phylANOVA, do the tip labels for the tree have t o correspond to the names of the groups (species) in the groups vector?

    1. Hi Peter. If I remember correctly, x should be a discrete character (such as character vector or factor) with names that correspond to the species names in the tree. It is also possible to conduct a similar analysis by fitting an 'generalized phylogenetic ANOVA' using gls. There should be information about that on my blog as well if you look around. - Liam