Tuesday, January 26, 2016

Learning “R” in Spain

Studying turtles with R. Julien Claude in the background.
The sun rising from Montserrat.
From January 17-23 my new PhD student A.J. Turner and I went to a small town near Barcelona in Cataluña, Spain. We were there to take a morphometrics course in R (more info here:Transmitting Science) . For the uninitiated, R is a programming language and environment that can used to manipulate data, conduct analyses, and make beautiful figures - among other things. We would like to use R to measure and compare shapes of various fish species to better understand how body shapes change over the life of an organism; how these shapes evolve among/between groups; and how to use information about shape to better understand the changing forms of of fishes over time. A.J. is quite clever and smart and he will one day be able to use this tool to make his cutting-edge dissertation even more cutting-edge. I was once clever and smart too but I’ve felt a little dumb post-tenure. I saw this class as an opportunity to retool, and to reshape (pun intended) some old projects and to think of new ones. It didn’t hurt that the course took place in beautiful Spain. The course was taught by Julien Claude, who is the author of a book “Morphometrics in R,” and he also wrote an R package called “ape” that has been cited thousands of times. There were about twenty other students from around the world there, some were studying shapes of dinosaur bones, or fruits, or flowers - among countless other projects. Almost all brought data to play with and manipulate. From 9am to 7pm for five days we were on our computers going through dozens of examples and exercises. It was rather intense, especially for me – not having been a student since I got my PhD almost 10 years ago. Except for some short breaks and meals, we were engrossed in R all day. The group of students and instructors were a disparate mix of international students, postdocs and PIs. Luckily everyone was very nice and A.J. and I ended up with twenty or so new friends and maybe some future co-authors. I particularly liked Julien. He and I share a rather silly and nerdy sense of humor. A running joke about one of the students being from the future and taking this class to destroy R like the Terminator had us giggling for days for some strange reason. (It might be that writing ten hours of computer code a day makes almost everything else hilarious.) Speaking of bad jokes: Do you know the favorite coding language of pirates? … R! ) By Day 4 my brain was full and I needed to take a bit of a break from the dark classroom and spend some time outdoors. A.J. and I got up at 5am and took a cab to the top of beautiful Montserrat and watched the sun rise over Cataluña. A.J. and I found ourselves walking around the grounds of a rather breathtaking Basilica at the top of Montserrat. There were monks chanting, bells ringing, and beautiful rows of multicolored candles lit for prayer. The sun rising over the mountains was stunningly beautiful as were the paintings and décor inside the monastery. The monastery has a famous dark skinned Virgin Mary statue that reminded us of this part of Spain’s rich African history. Cataluña houses an interesting mix of cultures, something that is notably distinct from the rest of Spain. We were often greeted with ‘Bom dia” in the morning (similar to the Portuguese “Bon dia”), and with “merci” in place of “gracias.” But alas we only had time to learn one new language, and we were back learning the grammar and culture of R in our classroom that same morning. In R we say hello like this setwd("/Users/Prosanta/Desktop/MorphometricswithR2016/datasets"). Our visit to Montserrat was just a few hours but luckily we also had a few free hours when we landed in Barcelona. My postdoc Fernando Alda is from Spain and I wouldn’t have been able to look him in the eyes if I didn’t tell him we saw at least some sites while we were in his home country. Luckily we were able to also see the Sagrada Familia on our way to the course on the day we landed. The Sagrada Familia is the infamously beautiful/hideous giant church designed by Spain’s most influential architect Antoni Gaudi. Inspired by biological shapes (apparently all biological shapes all at once), Gaudi initiated construction of this building in 1882 and it won’t be finished until 2020 (maybe). The building is impossible to describe with words, but let’s just say I don’t think Gaudi would have been good at R. Although I think our instructor Julien Claude can probably make anyone good at R.
               Julien is a patient and kind instructor who made sure every student was getting the current set of skills being taught before moving on; and he also understood that we each had different goals, projects, and kinds of data. For me learning elegant new tests of hypotheses for modularity (the independent changing of shape in one body part versus another) or fluctuating asymmetry (the unbalanced growth across a body’s axis of symmetry) were worth the price of admission. I already have new projects in mind and hope to help some students learn new morphometric techniques. A.J. and I are extremely grateful to our Department of Biological Sciences and Office of Research and Economic Development for the opportunity to attend the R class in morphometrics. 

A.J.Turner at La Sagrada Familia

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