Monitoring invasive alien species of Union concern

Adolf, Janne¹²³ Research Institute for Nature and Forest (INBO)⁴⁵

keywords: invasive alien species; monitoring schemes

Repository accompanying the development of monitoring schemes for the invasive alien species of Union concern in Flanders.

This is an overarching project repository. For a child repository concerning the Chinese muntjac, see the repository mias-muntjac.

Associated with this project is the following INBO publication:
Adolf, J., Strubbe, D., Adriaens, T., & Onkelinx, T. (2025). Prioritising invasive alien species for monitoring in Flanders: Results of an expert survey. (Rapporten van het Instituut voor Natuur- en Bosonderzoek; Nr. 59). Instituut voor Natuur- en Bosonderzoek. https://doi.org/10.21436/inbor.133486163

Repository structure

The repository is organised as follows:

.
├── data/processed
├── inst/
├── renv/
└── source/

data/processed

Contains processed data used in the project's analyses.

renv/

Contains files created by the renv R package to manage the R package environment and ensure reproducibility.

source/

Contains the source code for the project, including:

• analysis: R script to join species lists from GBIF and PrIUS
• export/survey_experts: scripts and files associated with the above cited expert survey, spanning all workflow phases (i.e., setup, distribution, data collection, data analysis, reporting). Scripts are R or JavaScript (automatically generated and to be deployed via Google Apps Script). The Quarto project and Quarto files used to generate the above cited publication are located in export/survey_experts/docu_report.
• functions: R functions used throughout the project
• gbif_occ_maps: R scripts for occurrence maps based on GBIF data
• presentation_ec: Quarto project and Quarto files used to generate an overview presentation over the project (contributing to the INBO-European Commission Invasive Alien Species Meeting on Oct 17, 2025)
• report: R scripts and R Markdown files associated with some early-stage documentation of the project

Reproducibility

This project uses renv to manage R package dependencies. The renv.lock file (and its commit history) provides detailed information on the R version and all R packages used. To restore the project dependencies from the lockfile, use the indicated R version and run:

renv::restore()

Footnotes

1. author ↩

2. contact person ↩

3. Research Institute for Nature and Forest (INBO) ↩

4. copyright holder ↩

5. funder ↩