Multilayer network analysis reveals connectivity synergies between protected area levels across various taxonomic groups

Datasets and codes associated to Prima, M.-C., Oliveira-Cruz, L., Miele, V., Si-Moussi, S., Rouveyrol, P., Suarez, L., & Thuiller, W. (2025) Multilayer network analysis reveals connectivity synergies between protected area levels across various taxonomic groups. Conservation Letters, 18:e13148. https://conbio.onlinelibrary.wiley.com/doi/10.1111/conl.13148 The « data » folder contains raw and derived data used in the analysis; the « output » folder contains data used to derive the results presented in: Prima, M.-C., Oliveira-Cruz, L., Miele, V., Si-Moussi, S., Rouveyrol, P., Suarez, L., & Thuiller, W. (under review). The organization of these folders and most of the scripts used in this study follow the pipeline of: Prima, M.-C., Renaud, J., Witté, I., Suarez, L., Rouveyrol, P., Fernando, M., Sacchi, A., Cosentino, F., Santini, L., Maiorano, L., Moreira, F., Dertien, J., Fernández, N., & Thuiller, W. (2024). A comprehensive framework to assess multi-species landscape connectivity. Methods in Ecology and Evolution, 15, 2385–2399. https://doi.org/10.1111/2041-210X.14444 The code of this pipeline is available from https://github.com/mcpri3/RFLC-SCP. This pipeline is made of four main steps, that are: Step 1. Clustering species in functional groups having similar traits and environmental niches (analyses/Rcode01_GetFunctionalGroups.R). Step 2. Generating resistance and habitat suitability maps for each group based on an ensemble of species distribution models (analyses/Rcode2_GetResisSuitMaps.R). Step 3. Generating ecological continuities per group (analyses/Rcode3_GetEcologicalContinuities.R). Step 4. Calculating multi-scale network metrics (analyses/Rcode4_GetConnectivityMetrics.R). Notably, we used the same steps 1 to 3. We have however updated step 4 to incorporate the multilayer network approach. This updated script is available here: analyses/Rcode4_GetConnectivityMetrics_MultilayerFramework.R. This script calls a function available in R/get.conn.metrics.R. The figures of the paper (and of the supplementary material) are available in the « figures » folder, the script to produce these figures is in the « analyses » folder.