BIOS2 Biodiversity Modelling 2025 Summer School collaboration repository

This repository provides resources and scripts for the Biodiversity Modelling 2025 summer school, with a focus on using the Madingley model. 🌍

The purpose is to facilitate collaboration and learning among students: run simulations, analyse results, and share reusable code. This is a living project — contributions are welcome! 🤝

You are encouraged to contribute by:

• 🧩 Adding reusable functions to the R/ folder.
• 📦 Packaging the project as an R package for better organization and sharing.
• 🎛️ Creating a Shiny app in the app/ folder to visualise simulation outputs.
• 📝 Writing vignettes in the vignettes/ folder to document workflows and collaboration guidelines.
• ▶️ Creating simulation scripts using the MadingleyR package in the scripts/ folder.

Getting Started

Cloning the repository

To get started, make sure you have Git installed and configured and then clone the repository

# Configure your Git username and email if you haven't already
git config --global user.name "Your Name"
git config --global user.email [email protected]

# Clone the repository
git clone https://github.com/bios2/biodiversity_modelling_2025.git

Working with the repository

You can work with the repository in your preferred R environment, such as RStudio, JupyterLab or vscode, or directly in R :

cd biodiversity_modelling_2025
R

Installation Instructions for local machine

Follow the instructions in the vignettes/installing_madingleyR.md file to install the madingleyR package and its dependencies on your local machine. This is essential for running biodiversity simulations using the Madingley model in R.

# Install the packages for package development
install.packages(c("devtools", "roxygen2", "testthat", "usethis"))

# Install shiny package if you haven't already
install.packages("shiny")

Run the demo simulation

# Load the package
library(MadingleyR)

source("scripts/demo_madingley.R")
# or run the demo script directly
# Rscript scripts/demo_madingley.R

Modifying the Madingley R code

Prerequisites: pull the latest version of the repository to ensure you have the most recent changes. Or a specific branch you want to work on. First make sure you have this project installed, otherwise clone it.

Then uninstall your current version of the package:

  try(detach("package:MadingleyR", unload = TRUE))
  try(remove.packages("MadingleyR"))

Then reinstall the package from the local source code:

library(remotes)
remotes::install_github(
  "bios2/biodiversity_modelling_2025",
  subdir = "MadingleyR-master/Package",
  build_vignettes = TRUE
)

#You can also get the pacakge from a specific branch like so
remotes::install_github(
  "bios2/biodiversity_modelling_2025@my-branch-name",
  subdir = "MadingleyR-master/Package",
  build_vignettes = TRUE
)

(UPDATE) If you get an error message at the end of the process, stating that your machine doesn't have the rights to move the temporary installation to the permanent repository, use this command before the install:

Sys.setenv(R_INSTALL_STAGED = FALSE)

You will now have the latest version of the madingleyR from the Bios2 workshop

Now if you want to modify a part of the package, you need to go inside the folder where you have the biodiversity_modelling_2025 repository and edit the files in the MadingleyR-master/Package/R/ folder.

After making changes, you need to reload your library:

devtools::load_all("YOUR_PATH/biodiversity_modelling_2025/MadingleyR-master/Package")

Important readings

• [Source code] Process raster data for madingley model
• [Paper]Model-based impact analysis of climate change and land-use intensification on trophic networks