Sunday, March 6, 2016

New version of phytools (0.5-20) submitted to CRAN

I have just submitted a new version of phytools (0.5-20) to CRAN. Obviously, it may not be accepted immediately by the CRAN gatekeepers - but, if not, hopefully we can get it online within the next few days. In the meantime, this version can also be installed directly from GitHub as follows:

library(devtools) ## devtools must be installed
install_github("liamrevell/phytools")

Updates from the previous CRAN version of phytools include, but are perhaps not restricted to:

  1. Update to read.newick to permit arguments to be passed by the user to scan.

  2. An alternative density tree plotting function, now called densityTree (1, 2).

  3. A new function (phylo.heatmap) for phylogenetic heat maps, suggested to me by a colleague Nate Swenson (1, 2, 3, 4, 5).

  4. A new function (dotTree) for plotting dots of different sizes to represent a continuous character trait at the tips of the tree (1, 2, 3).

  5. A new option to turn off the plotted points at the tips of the tree for objects of class "cophylo" (and other methods that use the same plotting function internally; 1, 2).

  6. Update to the traitgram plotting function phenogram to permit it to be used with nodelabels, etc. from ape.

  7. Update to phenogram to invisibly return the coordinates of the plotted tips.

  8. A new function (rootedge.to.singleton) which converts a tree with a root edge to one with singleton nodes; and updates to nodeHeights and nodeheight to include the root edge length.

  9. Some updates to the S3 plotting methods for objects of class "contMap" and "densityMap".

  10. Some changes to the argument default values in reroot (here).

  11. A version of dotTree for discretely valued characters (using different colors for different character states.

Here's a quick demo of the new phytools plotting function phylo.heatmap:

library(phytools)
packageVersion("phytools")
## [1] '0.5.20'
phylo.heatmap(tree,X,standardize=TRUE,pts=FALSE,lwd=2,
    labels=FALSE)

plot of chunk unnamed-chunk-2

Comments welcome!

1 comment:

  1. Evidently, it is already on CRAN (although no binary packages have yet been built).

    ReplyDelete