Thursday, November 17, 2011

phytools version 0.1-1

I just released the latest version of phytools to my website, here. The new features and functions of this version include:

1) A new function,, which allows the user to map temporal eras on the tree. More details in a prior post.

2) A user requested update to phyl.RMA() allowing for a fixed value of the λ parameter. More on this here.

3) A new function, brownieREML, which does much faster REML model fitting of the multiple rate Brownian evolution model of O'Meara et al. (2006). More on this here.

4) A couple of updates to phylosig() that allow the incorporation of sampling error into estimates of phylogenetic signal using K & λ. The method for including sampling error is based on Ives et al. (2007).

I also added a CITATION file. The CITATION file tells R how to respond to the function call:

> citation("phytools").

My CITATION file looks something like the following:

citHeader("To cite phytools in publication use:")
   title="phytools: An R package for phylogenetic comparative
      biology (and other things).",
   author="Liam J. Revell",
   textVersion=paste("Revell, L. J. (In press)","phytools: An R package for phylogenetic comparative biology (and other things)","Methods Ecol. Evol.")
citFooter("As phytools is continually evolving, you may want to cite its version number. Find it with 'help(package=phytools)'.")

and calls to citation("phytools") will now return the following:

> citation("phytools")

To cite phytools in publication use:

  Revell, L. J. (In press) phytools: An R package for phylogenetic
  comparative biology (and other things) Methods Ecol. Evol.

A BibTeX entry for LaTeX users is

    title = {phytools: An R package for phylogenetic comparative 
    biology (and other things).},
    author = {Liam J. Revell},
    year = {2012},
    url = {},

As phytools is continually evolving, you may want to cite its version number. Find it with 'help(package=phytools)'.



  1. The functionality added at each new version is so cool. Thanks for putting this together!

  2. Thanks for the comment!

    BTW, I meant to mention that I had to set citEntry(entry="Manual",...) in the CITATION file because if I set citEntry(entry="Article",...) it would not accept empty fields for publication volume & pages (information that is not yet available as the article is in press). I don't know of any way around this, but feedback is welcome.