Pacifica (autumnwinds) wrote,
Pacifica
autumnwinds

  • Mood:
Tyler and I just got back from a nearly week-long excursion to Idaho, for a wedding and some last-minute research stuff.

Thursday: Drive from Port Angeles to Seattle. Say hello to my mom, meet my Uncle Buck (from Arizona) for lunch (he had never met Tyler, and was unable to come to our wedding because he was recovering from stem cell therapy on his heart). Drove to Idaho.

Friday: Get breakfast at WinCo and a parking pass. Spend all day at school working on doing new data analyses. Can't find data block, so I create a new one (doing nearly the entire alignment by eye. Have lunch with Doc. Work with Niko and Jess to puzzle out how to run MrModelTest, then MrBayes, which is all command line and VERY finicky. Success. Go to College of Graduate Studies to get forms to fill out. Run new analyses in PAUP* for maximum likelihood, maximum parsimony, and minimum evolution (distance) with branch lengths. Success.

Saturday: Go to the last Farmer's Market of the season. Enjoy coffee with Doc and Carrie. Eat a tiny pumpkin pie. Return to school to rerun my PAUP* analyses because I forgot to run bootstrap analysis. Go back to the house and work on building my new trees. Arrange a cheese and cracker platter for a potluck. Go to Heidi and Andre's wedding reception at the American Legion cabin, and visit/dance with Emily, her parents, Pam and Marc, Heidi and Andre, etc. I have not seen most of these people since my own wedding or before.

Sunday: Eat pancakes for breakfast. naturamother and shaylith drive up from Lewiston and Orofino (respectively) and we spend a lovely day visiting while helping shaylith shope for new work clothes. Predictably, I buy something for myself (a long green coat). Go to Don, Cindy, and Sierra Kaag's house for a wonderful dinner that Tyler helps cook (I get a little bit of work done first). Visit with the Kaags and watch Best in Show.

Monday: Clean and roast all the pumpkin seeds from the pumpkin-exploding party at Doc's on Saturday (while we were at the wedding reception). Spend most of day working on analysis results while visitng in the herbarium. Realize that my Bayesian results are complete garbage. Have lunch with Jess. Chat with Cort about my garbage and confirm my suspicions. Talk to Jess. Figure out problem, successfully rerun MrBayes and get good results this time.

Tuesday: Show new results to Cort and get his approval. Spend most of day working on analysis. Go to One World Cafe for warm drinks. Walk back to school when I realize I forgot to do some stuff. Edit my GIS maps to include a new zoom and a new sample group. Double-check some specimen ID's. Go back to the house for dinner. Drive to every grocery store in town in unsuccessful attempt to find pumpkins for kids to carve. Visit happily with Doc and Carrie.

Wednesday: Drive back to Port Angeles in eight hours. Enjoy visits from seven trick-or-treaters, including one ninja turtle, and three preteen goth girls collecting candy in Hot Topic bags. Awesome.

P.S. Here is what I learned about MrBayes this week:
1. MrBayes cannot process data with colons, even if Sequencher uses colons to represent alignment gaps.
2. MrBayes cannot process data with apostrophes, even if Sequencher uses apostrophes to frame taxa names.
3. MrBayes needs your input file to read "inputfile.scores.txt", even if the manual says it's just "inputfiles.scores"
4. The first taxon in the list is treated as the outgroup, even if it's wrong.
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