Skip to content

Computer Tools for Ecological Research

2 ECTS Kourou Year 2 Semester 3 Compulsory Tool 1


This course is an introduction to different useful tools and handle ecological data and answer scientific questions. Students will first become familiar with the software R, used with the interface RStudio. Then other tools will be presented: R Markdow, Mendeley, and Git, to write reports, handle bibliography and track code versions.

Learning outcomes

By the end of the course, the students should be able to:

  • Use R to open a dataset, modify it, access specific parts of it, and write a new dataset. Write basics R commands, write loops and functions. Load R packages, be able to quickly use functions from new packages. Be aware of the main R packages that can be used to handle ecological data. Understand what is R and RStudio, how to link it with other tools (e.g., C++ or Git)
  • Write a report with R Markdown.
  • Use a software to handle the bibliography, add papers and other types of scientific reports, and add citations to it in their own reports.
  • Write a formatted report and be able to comply with guidelines for authors to write a paper.
  • Use a version control system to handle different versions of a project. Access and submit projects on GitHub.

Teaching and learning methods

Short introduction lectures and group class work to download and use the tools. Small data sets will be used as example. During their research projects, students will be encourage to use the tools, and ask for help or advises if needed.

Type of assessment

  • Group
  • Written assignment
  • Students will complete a project in groups of two or three. They will collect data and analyze it to answer a scientific question in tropical ecology. The students will have to use the tools presented in this module during their project and the grading of the project will take it into account: ability to identify the tools to use to achieve the different tasks of the project, implementation and execution of these tasks.


  • Location : Kourou
  • ECTS granting : AgroParisTech
  • Organisation : AgroParisTech


Mélaine Aubry-Kientz

Mélaine Aubry-Kientz

  • AgroParisTech, Kourou France