• Advanced Courses in Life Sciences

    Header of Ecology at Transmitting Science

Short Course – 3rd Edition

Species occurrence data download and cleaning with R

November 28th-29th, 2022

This course will be delivered live online

It will be taught using a combination of live (synchronous) sessions on Zoom and Slack.

The live sessions will be recorded and available to the participants for a limited period of time. However, attendance at the live sessions is required.

Course Obtaining and cleaning species occurrence data with RCourse overview

Species occurrence data are essential for a range of ecological and biogeographical analyses, from species distribution and ecological niche models to biotic regionalizations and global biodiversity trends.

Species occurrence data are now widely available in multiple online sources, although they are heterogeneous and come with caveats that need to be addressed before moving on with the analysis.

In this short course, we will use a range of tools to

1) Import species occurrence data from various sources into R (e.g. GBIF, iNaturalist, VertNet, EcoEngine, national / regional / continental atlases)

2) Join and arrange these data into a homogeneous dataset for analysis

3) Map and visually inspect the data for taxonomic and spatial errors and bias

4) Clean the data from detectable errors, using both non-automatic and automatic tools (e.g. ‘scrubr’, ‘CoordinateCleaner’)

5) Correct or minimize spatial biases with different tools (e.g. ‘spThin’, ‘humboldt.occ.rarefy’, ‘gridRecords’).

The course will be highly interactive and will include both theoretical and practical sessions. Participants are encouraged to work with their own species of interest, although several illustrative examples will also be provided.


Participants should have previous basic experience with R, a computer (Linux, Windows or MacOS) preferably with a webcam, and a good internet connection. A recent version of R will be needed, and RStudio is also recommended.




November 28th-29th, 2022

Schedule and Course length

Online live sessions Tuesday and Friday, from 15:00 to 19:00 (Madrid time zone).

8 hours




Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

A. Marcia Barbosa instructor for Transmitting Science

Dr. A. Márcia Barbosa

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science


  • Course Fee
  • Early bird (until October 31st, 2022):
  • 156 €
    (124.8 € for Ambassador Institutions)
  • Regular (after October 31st, 2022):
  • 196 €
    (156.8 € for Ambassador Institutions)
  • The price is VAT included.
    After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.


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