The Virtual Ecosystem data science repository

This repository is the data science repository for the Virtual Ecosystem project. It is used to store all the research and analysis being used to parameterise and run the Virtual Ecosystem model using git and GitHub to share all the code.

For details on using GitHub and git, please see the Wiki page here: GitHub overview

Getting started with the repository

The repository uses a reasonably complex set of tools to help ensure code quality assurance (QA) and common code formatting. You will need to follow some steps to get these tools working: see the wiki page on Getting Started

As a brief overview, this involves setting up the following tools:

• Python. Obviously, we use Python for running the virtual_ecosystem but it may also be used within this repository for analyses and we also require it to run some QA tools.
• Poetry. This is a Python package manager that we use to manage a shared set of Python packages used across the project.
• R. We will be using R extensively for analysis and data visualisation.
• renv. This is an R package manager that, like poetry, is being used to manage the shared set of R packages used across the project.
• pre-commit. This is a QA tool - we have a set of configured checks that run whenever you try and git commit some changes to the repo. If the changes fail any of the checks, then you will have to fix them and try again. Sometimes, the QA checks can automatically fix issues for you - in which case you just need to add the new changes to your commit and try again.

You will also notice a large number of small files with odd names in the repo. These are mostly used to configure the system - you can see more details on the what are these odd files wiki page