PASTA Tutorial:
Slides from my tutorial on PASTA.
Commands to set dendropy for PASTA (must be run from folder immediately above PASTA install folder).
Here are some random utilities I’ve put together in my life that others may find useful.
Color Palette Generator:
If you’ve ever used the RColorBrewer package and found that it just didn’t do enough for your tastes, this file might help. This lets you create a color palette where you specify an arbitrary number of gradations between colors and as many base colors as you need. For example, let’s say you want to plot lake acidity where the scale goes from red (for acids) to white (neutral) to blue (for bases), you can create a vector that describes those colors in gradations as fine as you’d like (currently the max is 51, but changing that is not complicated). The interpolation is linear on each of R, G and B, and all the calculations are shown. You can find some sample code implementing this in R here.
File: Color Palette Generator
Full-Year Calendar Generator:
Ok this is a simple one: type in a year (as far back as 1900) and this file will produce a one-page, printable calendar of the full-year. I keep a printout like this hanging near my desk for quick reference. Here’s an example of what it looks like, with the colors corresponding to the UIUC academic calendar in 2013: 2013 Calendar.