Growth of phylogenetics, or at least phylogen*

I'm working on slides for a job talk. I made one that might be of interest to readers of this blog, a plot of number of references with "phylogen*" in any field in Scopus through time (line on the figure, also the position of the blue circles). I also found the number of references with "evolution" or "ecolog*" as well as all combinations of these three terms to make Venn diagrams of the overlap of the terms (using Google Charts). It's interesting to see how the three areas overlap and change in size through time: "phylogen*" is now much more common (up to 38% of the frequency of "evolution") and now overlaps more with references with "ecolog*" than with references with "evolution". I'm sure there are all sort of artifacts and biases, but interesting to look at nonetheless. It does suggest that I should start thinking more about ecologists using TreeTapper.

Viewing missing methods/software, part IV: Sort of working

Well, I sort of have the visualization working. Users can choose which elements to graph (on Firefox) by dragging boxes to move them above or below a plotting line, and they can choose to limit to plotting only one of many options. See below.

On clicking the  update chart button, a tree is plotted using the Google Maps API, with branches colored based on whether they have no methods or software, methods but not software, or both methods and software [I originally had it update the map automatically on any change, but this is too slow]. Users can click on nodes to get an info window showing the choices made going from the tree root to the tips and links to any relevant software or methods. Just mousing over a node tells a user what option that node represents (i.e., "Treetype: Unrooted, polytomies, incomplete tree"). If a user has chosen just one setting for an option (as for criterion, below), the edge leading to that node is shorter and light gray edges are shown to indicate the options not examined.  See below (click to make larger).

The end product is beautiful and information-rich. It's also VERY slow. It takes literally minutes to generate the plot, and then >10 seconds between clicking on a node and getting the info window. Zooming in or out or moving the plot also take an agonizingly slow time. Getting info from the script that talks to the database to make code for the map takes a while, about 30 seconds, but the real slowdown comes when drawing the map. Google maps are slow with many markers and polylines: the map above has 221 markers and even more polylines, with the three circle polylines having 360 points each (using fewer makes a plot that's too rough). I'll have to decide what to do. I'd stayed away from Processing due to usability concerns, but it seems Google Maps isn't so great, either. I've read a little about generating image tiles rather than markers to speed up the map -- I'll look into this and other options. 

Google charts

I've added some Google charts to the front page of the TreeTapper site. I'm using googlechartseasyphpclass v 1.02 to more easily generate the code to call the charts (it involves converting numbers to letters for plotting, for one thing), though it does limit flexibility a bit (but the source code for the PHP script can be modified easily). YUI also has a new charts API, but it requires a very recent version of Flash for people to use (more recent than I had in FireFox) -- Google can simply create a png, which is convenient. The code to make the data to pass to the charts takes a little while to work (dozens of postgres calls): I might just update this daily and have the site call a saved version of the data. The charts I've made allow tracking of how much the database has grown in the previous month as well as breakdowns of references by year.