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Code repository for the SARS-CoV2 modelling initiative

The SARS-CoV2 Modelling Initiative is a loose conglomerate of scientists concerned about the outbreak of Covid 19. The main focus of the initiative is the situation in Germany. The scientific background of the initiative varies from epidemiologists, physicians, economists to mathematicians and physicists.

Click here to see the list of all packages.

This repository serves as a hub collecting code related to the initiative. This repository is no repository for code development, but a repository for code collection. All repositories are added via git subtree, and changes in the original repository are pulled in automatically.

If you are new to Git, see below.

Spreadsheet for parameters for modelling the spread of Covid-19

You would like to model the spread of Covid-19 mathematically? Then make sure to check out this spreadsheet with valuable information on parameter values.

What to achieve?

The objectives of this hub repository are

  • to provide a single point of reference,
  • to make your work transparent and accountable,
  • to allow for reproducibility, and
  • to reduce communication overhead.

How to contribute?

Suppose you would like to add your code to the repository. How do you do it? Basically, as soon as you have your code in a GitHub repository, you open an issue, and ask to be added. That's it. Or in some greater detail:

  1. Put your code in a GitHub repository. This means to put your code in a dedicated repository different from this repository.
  2. Open an issue, providing the following information:
    • programming language,
    • link to your repository, and
    • a contact e-mail address.
  3. Your code will be added to the repository via git subtree(see this post if you're interested in the technical details.)

Note: You have and will continue to have full control over your original code. Whenever you make changes to your original repository, these changes will be pulled automatically.

If you're a graphical mind, then think of the following picture:

All repositories contribute to this common repository, and all changes from all repositories will be pulled automatically.

Why Git/GitHub?

If you are unfamiliar with Git and/or GitHub, do not worry. As usual, new tools seem overly complex in the beginning, and one wonders "why bother with yet another new tool?" Generally speaking, Git is a version control system for source code; GitHub is a website that amplifies the collaborative aspect of using Git: it allows to comment on code changes, and serves as a single hub for every line of code. Another great advantage of GitHub is that it is a near-perfect implementation of if you see something, say something, meaning the following: if you find a typo or a bug, then you can fix it. GitHub is a great catalyst for self-correction.

Why bother with Git?

There are several advantages. Here's a list of personal favorites:

  • facilitate code review
  • track your progress
  • make code visible
  • introduce accountability
  • allow for collaboration
  • encourage clean(er) code

Regardless of why you use Git, it's one of these things where you wonder why you haven't heard of it before. Once you get the hang of it, you will not want to do without.

By the way: Git just turned 15.

New to Git/GitHub?

If you are a beginner, perhaps the most important idea to rectify is: Git is not GitHub. Git is a software that helps with source code control; GitHub is a website that uses Git and adds collaborative aspects.

The amount of tutorials for Git is seemingly endless. Here are three suggestions:

Plesae feel free to add to the list.


Repository for the SARS-CoV2 modelling initiative






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