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.<\/p>\n
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.<\/p>\n
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:<\/p>\n
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 <\/em>into Asteromphalus, <\/em>which means the former didn’t come up with any matches in Neptune when called from the matrix. Anyway,\u00a0I’m not sure I’ve been renaming things properly, so I need to go back and start that whole thing over…<\/p>\n For Mediaria, Campyloneis, <\/em>and Stictodiscus, <\/em>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 <\/em>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).<\/p>\n 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, <\/em>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<\/strong>, which suppresses converting strings to factors. Less memory-efficient, but appropriate.<\/p>\n 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.<\/p>\n","protected":false},"excerpt":{"rendered":" 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, […]<\/p>\n","protected":false},"author":2222,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1231,14607,13584],"tags":[19990,16233],"class_list":["post-1832","post","type-post","status-publish","format-standard","hentry","category-reflections","category-research-journal","category-timekeeping","tag-job-hunting","tag-morphospace"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/1832","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/users\/2222"}],"replies":[{"embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/comments?post=1832"}],"version-history":[{"count":5,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/1832\/revisions"}],"predecessor-version":[{"id":1834,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/1832\/revisions\/1834"}],"wp:attachment":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/media?parent=1832"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/categories?post=1832"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/tags?post=1832"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}