Code and data for the manuscript "Trophic Tug-of-War: Coexistence Mechanisms within and across Trophic Levels"

System requirements

• Software dependencies: R (has been tested with R version 4.2.2) and Python (has been tested with Python version 3.11.4).
• Required R packages:
  • tidyverse (version 1.3.2)
  • deSolve (version 1.0.1)
  • geomtextpath (version 0.1.1)
  • patchwork (version 1.1.0)
  • reticulate (version 1.28)
• Required Python packages:
  • numpy
  • pandas
  • matplotlib
  • scipy
• Required non-standard hardware: none.

Repository contents

• Reproduce.qmd. The main file (in Quarto) to reproduce the results of the manuscript. It contains the code to reproduce the figures of the manuscript.
• Reproduce.html. The html file provides an easy-to-read version of the main file.
• LV_multi_functions.py and numerical_NFD.py. Companion python file to Reproduce.qmd. It contains the functions to compute niche and fitness differences in Lotka-Volterra dynamics.
• Data directory. Contains the empirical data used in the manuscript. This data are from Sauve & Barraquand 2020.