• Advanced Courses in Life Sciences

    Header of Ecology at Transmitting Science

Short Live Online Course – 5th Edition

Species occurrence data download and cleaning with R

February 27th-29th, 2024

Live sessions will be recorded

Registration deadline: January 31st, 2024
Please note that registrations received after the deadline indicated above cannot be guaranteed a place on the course. If you wish to attend this course, please register at your earliest convenience

Course Obtaining and cleaning species occurrence data with R

Course 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.

Basic experience with R is required.

Participants are also required to have a computer with access to a good internet connection, a recent version of R and RStudio installed, and a set of R packages whose installation script will be provided before the course.

A. Marcia Barbosa instructor for Transmitting Science

Dr. A. Márcia Barbosa

Dates & Schedule

February 27th-29th, 2024

15:00-19:00 (Madrid time zone)

Online live sessions on 27 and 29 February, from 15:00 to 19:00 (Madrid time zone).

Total course hours: 8



This course will be delivered live online

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

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


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.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until November 30th, 2023):
  • 176 €
    (140.80 € for Ambassador Institutions)
  • Regular (after November 30th, 2023):
  • 270 €
    (216 € for Ambassador Institutions)
  • All prices include VAT.
    After registration you will receive confirmation of your acceptance in the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.


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