New test version of phytools (v0.2-02) with xkcdTree and new version of pgls.Ives

I just posted a new non-CRAN version of phytools (version 0.2-02). To install, just download phytools_0.2-02.tar.gz and install from source:

> install.packages("phytools_0.2-02.tar.gz",type="source", repos=NULL)
...
* installing *source* package 'phytools' ...
...
* DONE (phytools)
> require(phytools)
Loading required package: phytools
Loading required package: ape
...

With respect to phytools v0.2-01 this version has two additions:

1) An update to pgls.Ives. pgls.Ives implements the method of Ives et al. (2007) for phylogenetic regression with error in the estimation of species means. Basically, I was discovering that sometimes optimization failed due to the (arbitrarily specified) lower bounds required for σ_y² and σ_x² by the optimization method, optim(...,method="L-BFGS-B"). I have now decreased the default value for these bounds (by a factor of 10e-4) and also allow user control. Other aspects of control of optim are still not under user control, so I will change that. The function now also returns convergence and message from optim (basically optim's report on whether or not it thinks it has converged).

2) I have added the function xkcdTree to the phytools package. I documented xkcdTree in several prior posts (1, 2, 3, 4, 5) and I won't repeat that documentation here. Suffice it to say that the function plots a phylogenetic tree in the style of xkcd style graph (in other words, hand drawn with a particular all-caps style of font). I decided to develop this function on a whim and without any real intention of adding it to phytools, but it generated a huge amount of traffic to my blog (with many visitors coming from several a number of tweets that my posts on this function stimulated, see below).

Consequently, I have added the function to phytools with the following caveats:
a) phytools users wanting to plot xkcd style trees with phytools will first need to download and install the font 'xkcd.ttf' (just search for it);
b) users will also have to download and install the CRAN package extrafont and its dependencies - phytools will not load these dependencies of xkcdTree automatically; and
c) at least Windows users of R will have to download and install Ghostscript - this is required to embed the xkcd font into the PDF file with your tree.

Hopefully, xkcdTree will return a sensible error if you try to run it but have not taken one of the above three steps!

xkcdTree can be called on its own, or through fancyTree(...,type="xkcd").

With respect to the latest CRAN release of phytools, this new package version also has two more new functions: fastAnc and matchNodes (see 1 & 2), as well as updates to a number of other functions that now call fastAnc instead of the much slower (and sometimes quite inaccurate) anc.ML.