Siliceous and Delicious

Perhaps my first success of my PhD. Just before noon this day, the eighteenth of August of the year two thousand and eleven of our common era, I completed coding the last of the 138 diatom genera… At last, a data set. I thought I’d use the opportunity to pick up my journaling here to keep a better record of my progress, ideas, and so forth.

Spent quite a while being somewhat dumbstruck about what to do next—the clear path ahead of “plod through the characters” has suddenly come to an end, and I need to switch the thinking brain on again to determine what path ahead to pick out next. Decided that the first step should be a bit of cleaning up of the data—adjusting some of the characters, taking out the ones that are clearly silly, etc. Once I started doing that, I realized that the more important thing to do was to get the data imported to R, and work from there.

Took me a while to get back into the swing of things, but by a quarter to six I had imported the data, and written a little routine to calculate the %age of taxa with valid character states for each character—i.e. what proportion of the total list of taxa have values that aren’t “n/a” or “?” for each character. Slam! First step in the analysis. Done. Pat on back, jump on bike, pick up Kati from work.