Nordic Oikos 2018 - R workshop

Scientific reuse of openly published biodiversity information: Programmatic access to and analysis of primary biodiversity information using R. Nordic Oikos 2018, pre-conference R workshop. Two-day workshop, Sunday 18 February and Monday 19 February 2018.

ForBio Research School in Biosystematics

Scientific use of openly published and aggregated primary biodiversity information is in steady increase. Reuse of open research data and academic data citation is an emerging trend that is prioritized by current research policies, and citation of biodiversity data published through the Global Biodiversity Information Facility ( shows a steady upward trend. On-going improvements in biodiversity informatics to build support for new data types, such as the recent event-core in GBIF, open up for new uses of GBIF-mediated data. However, many researchers still access biodiversity data in GBIF from the web portal and the advanced machine readable programming interfaces (APIs) remain arguably underutilized. This Oikos 2018 workshop will introduce participants to the GBIF API and stimulate Nordic ecologists and systematists to a more programmatic use of GBIF data. Most examples and training exercises will use the R language and software environment for statistical computing. Scientific workflows with tools such as Galaxy will not be covered in this workshop. However, the interested workshop participant will be gently guided towards further reading material. The workshop is organized by the Norwegian participant node in GBIF ( and the ForBio Research School in Biosystematics (, both hosted by the UiO Natural History Museum in Oslo and will take place on Sunday 2018-02-18 and Monday 2018-02-19 at the Oikos conference venue Trondheim. Registration is open for both Oikos 2018 participants and ForBio members. We plan to spend some time to work in groups with hands-on exercises, so please consider bringing your own data and research questions to the workshop. We will also prepare some training datasets for you to work with.

Workshop sessions include:

Session 1: Quick introduction to GBIF and biodiversity informatics

Session 2: Quick intro to R, RStudio, GitHub

Session 3: Download occurrence data from GBIF using rgbif

Session 4: Download event data et al. from GBIF / IPT and retrieve associated information

Session 5: Linking GBIF data with environmental layers

Pre-liminary schedule

Sunday 18 February

10:00 Introduction to workshop, round-table expectations & R-experience

10:15 Session 1 - Introduction to GBIF and biodiversity informatics (ca 45 min)

11:00 Short break (coffee)

11:15 Session 2 - Introduction to R, RStudio, GitHub, and R Markup (ca 45 min)

12:00 Lunch

13:00 Session 3 - Download occurrence data from GBIF (ca 60 min)

14:00 Session 3 Exercisesdownload GBIF data and import in R

15:00 Session 4 - Download event-core data (etc) directly from IPT (ca 60 min)

16:00 Session 4 Exercises - Download datasets from GBIF

17:00 End day 1


Monday 19 February

09:00 Summary and status from day 1, round-table

09:30 Session 4 Exercises - Download event-core data (etc)

12:00 Lunch

13:00 Session 5 - Link environment layers to GBIF occurrences (ca 60 min)

14:00 Session 5 Exercises - Link GBIF data with environment layers

15:00 End workshop ca 15:00

17:00 Registration and reception for the Nordic Oikos 2018 conference

Workshop venue: 

The workshop will be at Realfagbygget, NTNU (not a the same location as the Nordic Oikos 2018 conference at Clarion) in Trondheim.

Auditorium DU2-150 [50 persons] and break-out room EU2-145 [20 persons] at Realfagsbygget (lower floor U2).

NTNU Gløshaugen campusHøgskoleringen 5, NO-7491 Trondheim, Norway (latitude 63.415275, longitude 10.406295).

Travel guide:

From the airport in Trondheim (Værnes airport, TRD) to the city you may choose between two different airport shuttle services, Flybussen/Nettbuss and Værnes-ekspressen, with departure schedule ca every 10 minute. You may also choose the airport train, with travel schedule ca every 1 hour on weekdays, ca every 2 hour in weekends. The train station downtown Trondheim is a short walk (450 m) from the Nordic Oikos conference venue, BUT approximately 3 km from the NTNU university campus where the pre-conference workshops are organized. Both airport buss alternatives drive pass by the NTNU university campus. The closest stopping places are "Professor Brochs Gate" (500 meter, 6 minute walk) or "Lerkendal Stadium" (600 m, 7 minute walk).

Hotel close to the venue for the pre-conference workshop: Scandic Lerkendal at Klæbuveien 127, NO-7031 Trondheim, Norway. Which is a short 8 minute walk from the workshop venue at NTNU Realfagsbygget, Høyskoleringen 5.



GBIF R workshop February 18-19 2018
Take the blue pill, and let BIG DATA sooth you back to sleep -- or take the red pill and join us for a two-day session of programmatic access to GBIF data using R - to tame the bigOpenData beast,


Workshop organizers: Dag Endresen and Anders Finstad (Global Biodiversity Information Facility Norway,, and Hugo de Boer (ForBio Research School in Biosystematics). Markus Skyttner (Swedish Museum of Natural History, representing and Erlend B. Nilsen (Norsk institutt for naturforskning, NINA) contributes to the teaching at the workshop.


Tags: GBIF, R, rgbif, rOpenSci, GitHub, sampling event, event core, Biodiversity informatics, Darwin Core
Published Sep. 30, 2017 9:50 AM - Last modified Mar. 9, 2018 9:06 AM