The Scientific Committee on Antarctic Research (www.scar.org) is pleased to partner with the rOpenSci project and the Antarctic Biodiversity Portal (www.biodiversity.aq) in organising a short course on tools for Southern Ocean spatial analysis and modelling using R. This course will teach participants how to retrieve, model and interpret species occurrence data from the Southern Ocean using R-tools developed through the Antarctic R community. In hands-on sessions, participants will learn how to find, download and clean data using R packages and how to display these data on Antarctic (polar projection) maps. The course will introduce various ways of analyzing the data including Species Distribution Modelling (SDM).
Our aim is that by the end of the course students will be equipped to:
- Set up a workflow for the retrieval, cleaning and analysis of Southern Ocean biological data
- Learn which R packages can be used to do this
- Learn about species distribution models and how to develop them
- Apply these new insights to their own data.
See https://scar.github.io/EGABIcourse19/.
Anton Van de Putte (Royal Belgian Institute for Natural Sciences, KULeuven) manages the SCAR Antarctic Biodiversity Portal and is a strong advocate of FAIR data and reproducible science. You can ask him questions about biological open data standards and data cleaning.
Charlène Guillaumot (ULB, Bruxelles) is an ecological modeller.She studies the potential and limits of species distribution models and dynamic energy budget models on Southern Ocean case studies, and develops/adapts methodologies according to the encountered issues.
Grant Humphries (HiDef Aerial Surveying Ltd) is a seabird biologist and data scientist who has worked on terrestrial and marine ecosystems with a focus on applying machine learning to complex ecosystems. You can chat with Grant about creating decision support tools in R and Python, and what his favourite programming language is.
Ryan Reisinger (CEBC-CNRS) is an ecologist who models the movement behaviour, habitat use and distribution of marine predators, using telemetry and biologging data.
Ben Raymond (Australian Antarctic Division and the University of Tasmania) is a data-focused research scientist working across a range of Antarctic and Southern Ocean science. He is a co-proponent of the SCAR/rOpenSci R community initiative (https://scar.github.io/ropensci/)
Huw Griffiths (British Antarctic Survey) is a marine biologist who studies large-scale biogeographic and ecological patterns in space and time. He uses selected groups of animals to investigate trends in distribution in the Polar Regions, utilising large biological and physical databases to understand key processes.
The first part of the course (3 days) will focus on introducing various R packages and overall workflows. The second part of the course (2 days) will be a hands-on opportunity for participants to work on their own data with the assistance of the course instructors. You can choose to only register for the first part of the course if you prefer. The course is targeting Polar Early Career scientists, but is open to any other research students or scientists that require these skills for their work. There is space for a maximum of 20 participants.
The course will generally run from 9am to 5:30pm each day, with breaks throughout the day for refreshments and discussion. See the course schedule.
The course will take place at the Meeting Room of the Collegium Veteranorum (Cove 02.10)
Sint-Michielstraat 2-4
3000 Leuven
Some experience in the computer language R is desirable, and experience with GIS is helpful.
For the course particpipants should bring
- their own personal laptop
- Headphones
Please make sure you have installed
Feel free to also install QGIS https://www.qgis.org/en/site/ and Quantarctica http://quantarctica.npolar.no
GGIS is a free, cross-platform, open-source software that allows to create, edit, visualise, analyse and publish geospatial information/ Quantarctica is a collection of Antarctic geographical datasets which works with theQGIS software.
If you are not sure if your experience in R is sufficient, you should follow the one of the free online courses below:
https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro/
https://obis.org/manual/intror/
English
To ensure a safe, enjoyable, and friendly experience for everyone who participates, we have a strict code of conduct that all participants are expected to follow.
Applications for the course are closed. If you have questions or suggestions you can create an issue here. Alternatively you can contact datascience.biodiversity.aq (at) gmail.com
rOpenSci is a non-profit initiative founded in 2011 to make scientific data retrieval reproducible, and fosters a culture that values open and reproducible research using shared data and reusable software. rOpenSci maintains a number of widely used R packages, creates social infrastructure through a welcoming and diverse community, builds capacity and advocates for a culture of data sharing and reusable software.
The Expert Group on Antarctic Biodiversity Informatics aims to foster the application and development of biodiversity informatics (computationally-driven biodiversity science and information processing) in the Antarctic scientific community.
The Antarctic Biodiversity Portal offers access to Antarctic Biodiversity data. It is one of the federal Belgian contributions to LifeWatch-ERIC: a European Infrastructure Consortium providing e-Science research facilities to scientists seeking to increase our knowledge and deepen our understanding of biodiversity organisation and ecosystem functions and services.