Thursday, December 26, 2013

Three years of blogging

It's now been three years since I starting blogging about phylogeny methods on (originally - and so, in the tradition of 2011 and 2012, I thought I'd spend a few minutes talking about what I did this year in the phytools package and on the blog.

According to the (somewhat dubious, in my opinion) page stats, the phytools blog received upwards of 150,000 page views in 2013. Even if 1/2 of these were by bots, that is still quite an impressive tally. Certainly, by any measure the popularity of the phytools blog as a free repository of information about phytools and phylogeny methods has increased over the past year.

Towards the end of 2012 and throughout 2013 I added considerably to the plotting capabilities of phytools (evidenced, in part, by my recent MEE paper on some new plotting methods). Consequently, it's no great surprise that two of the most viewed phytools blog posts of 2013 included the description of a new method to visualize uncertainty on a traitgram, and some of the description and illustration of the new plotting functions contMap and densityMap, including this description of a published use of both methods in the same figure (which probably didn't hurt by having been re-tweeted by @systbiol). Nestled also among the top three most popular blog posts of 2013 was this comment on why we don't normally expect the residuals from phylogenetic ANOVA or regression to be normally distributed. Also popular were a wide range of posts about stochastic mapping and ancestral state reconstruction, including information about a new method based on the the threshold model from evolutionary quantitative genetics.

Towards the end of 2013, I started on a new project Rhylip. The purpose of Rphylip is to create an R interface for all 30+ programs in the PHYLIP phylogeny method software package by Joe Felsenstein. This will hopefully allow the many functions of PHYLIP to be used seamlessly within an integrated R workflow. (Here's an example of Rphylip at work - created for my phylogeny methods class using knitr.) I'm about 50% of the way there, so I hope to get this done soon.

Finally, I recently learned that my CAREER proposal to do phylogeny method research in several new areas has been recommended for funding by the NSF DEB Systematic Biology program. (Prospective students & postdocs take notice - I will be hiring in 2014!) This comes exactly at the right time as my start-up is in its dying breaths right now. Interestingly, part of the original ulterior motive in developing this blog back towards the end of 2010 was as a supporting 'broader impact' for what was at that time my first attempt to acquire funding for phylogeny method research from the NSF. Thus, the NSF is in part responsible for this blog & phytools as a community resource even without having funded it! (Until now, that is.)

Happy 2014 & thanks for reading!


  1. Liam, Congratulations on the NSF grant and for 3 years of blogging. Your blog and software are outstanding resources for the phylogenetics community.
    Tony Gamble

  2. Congrats on both Liam, and keep up the excellent work!!