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spacemodR

Documentation

Spacemod Habitat, Trophic, Dispersal, Exposure and Risk Mapping

spacemodR is an R package designed for spatial ecological risk modeling. It integrates habitats, trophic webs, dispersal, and contaminant exposure to build complex “spacemodels” linking geographic data (rasters, vectors) with biological interactions.

📦 Installation

The package is automatically built via GitHub Actions. You can install it by retrieving the archive generated by the continuous integration system.

Note about tracking big files with git

To git track big files, we use git lfs. Before using git add for a specifi file, we have to git lfs track it like this:

git lfs track "raw_data/new_fit.rda"

Via GitHub Action Artifact

The .github/workflows/build_and_release.yaml workflow is configured to build the package and check its integrity on every push to the main branch. To install the latest version:

  1. Go to the Actions tab of the GitHub repository.
  2. Click on the latest run of the “Build and Archive” workflow.
  3. At the bottom of the page, in the Artifacts section, download the spacemodR-archive file.
  4. Unzip the file to obtain the .tar.gz source file.
  5. Install the package in R using the following command:
# Replace the path with the location of your downloaded file
install.packages("path/to/spacemodR_0.1.0.tar.gz", repos = NULL, type = "source")

Note: Ensure that system dependencies (GDAL, PROJ, GEOS) are installed, as the package depends on sf and terra.

Using the docker file 

docker build -t spacemodr .
docker run --rm -ti \
  -p 8787:8787 \
  -e PASSWORD=mdp \
  -v /home/virgile/Downloads:/home/rstudio/data \
  spacemodr

Go to http://localhost:8787, where user is rstudio and password: mdp.