The purpose of this work was to develop several tools and metrics to identify and characterize the biogeographical structure of a region. As described in the paper [1], we applied this method to unveil multiscale biogeographical structures in plant species distribution in the south of France. We also developed an interactive web application to visualize the results.
The test-value matrix described in [1] is available in the csv file rho.csv. The table contains 11 columns with column names, the value separator is a semicolon ";". Each row represents a plant species.
- ID: SILENE ID of the plant species
- Name: Name of the plant species
- Test value bioregion 1: Contribution of the plant species to cluster "Gulf of Lion coast"
- Test value bioregion 2: Contribution of the plant species to cluster "Cork oak zone"
- Test value bioregion 3: Contribution of the plant species to cluster "Mediterranean lowlands"
- Test value bioregion 4: Contribution of the plant species to cluster "Mediterranean borders"
- Test value bioregion 5: Contribution of the plant species to cluster "Cévennes sensu lato"
- Test value bioregion 6: Contribution of the plant species to cluster "Subatlantic mountains"
- Test value bioregion 7: Contribution of the plant species to cluster "Pre-Alps and other medium mountains"
- Test value bioregion 8: Contribution of the plant species to cluster "High mountains"
- Species group: ID of the plant species group the plant species belongs to.
The function biogeonet (contained in the script biogeonet.R) allows the user to compute the matrices rho and lambda as described in [1]. The input of the function is a three-column data frame where each line gives the presence of a given species in a given cell (and its associated bioregion). An example of input data is available in the file test_biogeonet.Rdata. The first column is the SILENE ID of the plant species, the second column is the ID of the 5x5 km^2 cell where the species is present, and the third column represents the bioregion the cell belongs to (obtained with OSLOM).
The folder Vizu contains all the material (R scripts, Rdata and www data folder) needed to run the app.
If you use this code, please cite the following reference:
[1] Lenormand et al. (2019) Biogeographical network analysis of plant species distribution in the Mediterranean region. Ecology & Evolution 9, 237-250.
If you need help, find a bug, want to give me advice or feedback, please contact me!
We recently developed an R package to facilitate the use of this function (and more) with R.
This repository is mirrored on both GitLab and GitHub. You can access it via the following links:
- GitLab: https://gitlab.com/maximelenormand/Biogeographical-network-analysis
- GitHub: https://github.com/maximelenormand/Biogeographical-network-analysis
The repository is archived in Software Heritage: