Saturday, February 25, 2012

New version of phytools submitted to CRAN

I just submitted a new version of phytools (v0.1-7) to CRAN. Assuming this version is approved, it will most likely percolate onto the CRAN mirrors within a few days.

New features relative to the last CRAN version of phytools include the following (in no particular order):

1) A new function, findMRCA, which uses the ape function mrca and phytools function nodeHeights to find the set of MRCAs for a list of tips. If findMRCA(tree,tips=NULL) (the default) then the function just returns mrca(tree). My blog post about this function is here.

2) An update to plotSimmap in which the underscore character, "_" is swapped for a blank space (i.e., " ") in tip labels for plotting. Note, this will also affect plotTree. I wrote about how this could be done externally to the function here, and Dave Bapst suggested I add this to the function - and now I have.

3) A new function called paintSubTree that is described here and here.

4) A new version of phylosig in which control of multivariate optimization for phylosig(...,method="lambda",se!=NULL) is migrated to the user. I also made some attempt to improve the default starting values for optimization under this model. These changes are described here (with the bug report that inspired it here).

5) A new version of phyl.RMA for phylogenetic major axis regression which also includes hypothesis testing about the regression slope. This is described here. This change was requested by a phytools user.

6) A new version of phenogram which allows the user to control the axis dimensions. This update was motivated by a user request and is described here.

7) A major update to brownie.lite which allows the incorporation of information about intraspecific sampling error following Ives et al. (2007). This involved a total re-write of the function. The new version is described here. The function is, of course, based on the method by O'Meara et al. (2006).

9) An update to plotSimmap which allows the user to plot node numbers for internal branching points in the tree. This is described here.

10) A minor change to plotTree, now really just a wrapper for plotSimmap, which allows it to inherit the ability of plotSimmap to plot node numbers.

I think that's about it. Hopefully the new version of phytools will be available from CRAN shortly. (Check the phytools CRAN page.) In the meantime, interested users can also download the package source here and install as follows:

> install.packages("phytools_0.1-7.tar.gz",type="source", repos=NULL)

Thanks for trying out phytools and reporting bugs!

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