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📦 Data and R code to explore the individual and interactive effects of enrichment and temperature on food-web structure in lakes and streams - Bonnaffé et al. (2024) [https://doi.org/10.1111/ele.14480]

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FoodWebsLakeStream

📦 Scripts and data for reproducing the results obtained by Willem Bonnaffé ORCID iD icon, Alain Danet ORCID iD icon, Camille Leclerc ORCID iD icon, Victor Frossard ORCID iD icon, Eric Edeline ORCID iD icon, and Arnaud Sentis ORCID iD icon in the paper "The interaction between warming and enrichment accelerates food-web simplification in freshwater systems".


Repository overview

This repository is structured as follow:

📁 FoodWebsRiverLake/ (root of the compendium)
├── 📁 data/ (contains data, arranged by type: raw and derived)
│       ├── 📁 derived-data/ (contains modified data derived from raw-data)
│       └── 📁 raw-data/ (read-only data and should never be changed)
├── 📁 doc/ (contains documents related to the project (e.g., pdf from an .Rmd file))
├── 📁 figs/ (contains figures related to the project)
├── 📁 statistical_analysis/ (contains all files related to statistical analysis)
├── 📁 R/ (contains the R functions)
└── 📁 vignettes/ (contains Rmd files for running specific analysis (e.g. metaweb reconstruction))

Please note that the 📁 statistical_analysis/ includes a README.md file with specific instructions for analysis. Additionally, both the 📁 derived-data/ and the 📁 raw-data/ contain their own README.md files, which provide details about the data files.

Running instructions

Used softwares:

version 4.2.2 or greater

version 2022.12.0 or greater

  • Install (if necessary) and load all required packages
  • Load all required functions

Additional resources

  • Bonnaffé, W., Danet, A., Legendre, S. & Edeline, E. (2021). Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level. Oikos, 130, 1297–1309. https://doi.org/10.1111/oik.08173.
  • Danet, A., Mouchet, M., Bonnaffé, W., Thébault, E. & Fontaine, C. (2021). Species richness and food-web structure jointly drive community biomass and its temporal stability in fish communities. Ecol. Lett., 24, 2364–2377. https://doi.org/10.1111/ele.13857. Associated compendium: fishcom.
  • SizeTrophicInteractions to compile and estimate (if necessary) of the individual body size of the fish.

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📦 Data and R code to explore the individual and interactive effects of enrichment and temperature on food-web structure in lakes and streams - Bonnaffé et al. (2024) [https://doi.org/10.1111/ele.14480]

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