Documentation for the OBIS Species Distribution Models (part of the MPA Europe project)

Documentation for the OBIS contribution to MPA Europe (WP3): species distribution models (SDMs), diversity metrics and habitat maps for European marine species.

The rendered documentation is available at https://iobis.github.io/mpaeu_docs.

Contents

The documentation is a Quarto book (see _quarto.yml). Chapters, in order:

File	Content
index.qmd	Introduction
studyarea.qmd	Definition of the study area
sdms.qmd	The SDM framework and the modelling workflow
datadownload.qmd	Species list, occurrence data and quality control
datamining.qmd	Additional biodiversity data (literature, repositories, GBIF)
datause.qmd	How to access and use the models (map platform, AWS, STAC)
understanding.qmd	How to interpret SDM outputs
citations.qmd	Datasets used (loaded from datasets_citation.json in mpaeu_sdm)

methods-testing.qmd and results.qmd are kept in the repository but currently not included in the book (they are commented out in _quarto.yml).

Related repositories

• iobis/mpaeu_sdm: code to run the modelling pipeline
• iobis/mpaeu_msdm: the obissdm R package
• iobis/mpaeu_maps: data access and how to cite the product
• iobis/mpaeu_studyarea: study area shapefiles

Building the docs

quarto render

Output goes to docs/ (used by GitHub Pages). Computation results are cached in _freeze/. Some chapters read example model outputs from files/results, which are not fetched by the render.

Project status

The MPA Europe project concluded in 2025. The documentation describes the modelling as done in version 2 of the SDMs (concluded in August 2025). See the mpaeu_sdm NEWS for later code changes.