Siliceous and Delicious

Had a very reassuring meeting with Andy this morning, who was very excited about the morphospace results I showed him and appeared to be very optimistic about their potential to form both a “good thesis chapter and a good paper”. We also discussed how to proceed with the book chapters the PlanktonTech Germans had requested, and each (later on in the day) submitted an outline for a chapter to them. Done.

Buoyed by that morning conversation, I went along to the Job Acceleration Workgroup meeting, which was mostly about “elevator pitches” (not very useful for me, as I don’t really know what I’m angling for yet, but illuminating to see how difficult it is) and the schedule for the weeks ahead. Crucially, I had a great conversation on the way out with a fellow PhDer who was also interested in consulting but has become quite disillusioned with the idea; it was nice to make contact with a kindred spirit.

Later in the afternoon, I returned to R to press ahead with the morphospace and address some of the major problems I ran into late yesterday. Mainly these centered on the genus names in Neptune not matching the genus names in my morphospace. I discovered, and fixed, further errors in Neptune:

1. Aulacoseira is misspelled as Aulacosira in Neptune.
2. According to my notes Bolli says it’s Lisitzinia after all, so I changed it back.

Unfortunately, something with the factors was going very wrong, and I now have to go back over what I did yesterday and start again. I had also accidentally merged Liriogramma into Asteromphalus, which means the former didn’t come up with any matches in Neptune when called from the matrix. Anyway, I’m not sure I’ve been renaming things properly, so I need to go back and start that whole thing over…

For Mediaria, Campyloneis, and Stictodiscus, I also had two entries each in the matrix, to distinguish between different valve morphologies. This doesn’t work with the Neptune integration, since I can only have a 1-1 mapping, so I took the triangular form of Stictodiscus and the raphe valve of the other two and threw the other lines out of the matrix for the reanalysis. I just removed those lines out of the .txt file which I call from R (they’re still in the .numbers file for future analysis).

The solution to the renaming problem was simple but profound (aren’t they always?): my genus names were being stored in the data frame as factors, so trying to change the value of an entry or set of entries to a string not found in the factor levels caused a problem. The solution was simply to read in the data frame from file using the read.table option as.is=TRUE, which suppresses converting strings to factors. Less memory-efficient, but appropriate.

Fixed the names, but since re-running the distance matrix was going to take some time, decided to head home at 5:20 and let it run there.