Written by: Johannes De Groeve
Partner institute: Fondazione Edmund Mach – Ghent University
Phd project: A wildlife journey in space and time: methodological advancements in the assessment and analysis of spatiotemporal patterns of animal movement in a changing European environment.
In the last week of September (25-29) I attended the course ‘Interactive Data Analysis and Visualization with R Shiny‘, organized by Transmitting Science near Barcelona, Spain. Specifically, we were hosted in a small and quiet village named Els Hostalets de Pierola, approximately half an hour from Barcelona, situated on a hill with a spectacular view of Montserrat, a famous mountain and landmark of Spain. The region in which the village is situated is well-known among geologists for its fossils dating back to the Mioceen, including plenty remains of mammals and reptiles and even of a Mioceen primate, the Pierolapithecus catalaunicus, discovered in 2002. The surrounding landscape is stunning: a fragmented landscape, with small canyons, forested hills and slopes covered by olive trees and vineyards. We were hosted in a youth hostel and the course was held in a venue 5 minutes walking from the accommodation.
The course was for people interested in developing R Shiny applications to deliver their research. The main goal was to teach the skills necessary to translate static into dynamic products delivered via simple web-based graphic-user interface. Shiny is extremely powerful and allows to make any R product interactive. Nowadays, thanks to its user friendliness, Shiny is gaining in popularity, especially in the USA where apps are even developed by newspapers to present interactive maps, tables and graphs. Since recently the R Shiny people also developed great tutorials to get started: https://shiny.rstudio.com/tutorial/.
During the course, our teacher Dr. Ashton Drew, taught us how to use available Shiny tools (i.e., widgets, such as slider bars, check boxes, pick lists) and other interactive features to make plots and tables interactive. Obtained knowledge was first applied to a provided dataset, and then, attendees could work on their own projects. I eagerly started to built my first interactive application of a methodology that I have developed in course of my PhD. Specifically, I built a prototype of an interactive tree-based application that makes use of Sequence Analysis Methods (SAM), derived from molecular biology, to explore, identify and classify ecologically relevant and similar sequential patterns in habitat use by animals. In the prototype of my app several parameters can be set interactively: temporal resolution and range of the sequences, number and classification of habitat use classes, environmental layers to visualize, etc. Currently the app is still in development, but once ready I will update the IRSAE community.
The course completely met my expectations. In a very short time I have learned so much and managed to built a prototype of a fairly complex app. The group was small and very diverse. In total we were seven students, all from different disciplines (engineering, zoology, bioinformatics, remote sensing, conservation, movement ecology,…) and different research levels (PhD candidates, postdocs, senior researchers). The organizers of this Transmitting Science course, Ana Rosa Gomez-Cano, Soledad De Esteban-Trivigno and her husband Juan Vicente Berto-Menqual, helped to make this a great experience. Several side activities were organized, including a hike, a visit to the paleotological museum and to a cava winery and finally a barbecue in the garden of Soledad and Juan. During lunch we also learned to know the local Spanish food, which was deliciously prepared by Juan.
To conclude, I highly recommend to any IRSAE student to have a look at the courses offered by Transmitting Science (http://www.transmittingscience.org/courses/). IRSAE students have a 20% discount to any course.