Models

Model source code, documentation, and interactive plots. All code presented here is made available under permissive licenses. Please check each respository for details. I am currently working on Git is my lab book, a collection of materials to support early- and mid-career researchers who want to develop their computing skills and make effective use of available tools and infrastructure.

A User's Guide to Infectious Disease Modelling

The PRISM2 CRE published A User's Guide to Infectious Disease Modelling in 2016. This provides an introduction to interpreting the results of mathematical modelling studies in epidemiology. The primary target audience is policy makers who want to capitalise on these kinds of studies to inform immunisation policy and the control of vaccine preventable diseases.

Interactive epidemic models

Renal physiology models

Before I came to infectious diseases epidemiology, I modelled how kidneys regulate water and salt balance.

Making models accessible and useful

As mathematical models grow larger and more complex they become harder to analyse and understand. Once a model is sufficiently complex, the likelihood of someone being able to replicate its behaviour based on the model description in a publication becomes negligible. Making the model source code available is necessary but insufficient to render a model comprehensible. This has led to a proliferation of semantic markup languages and detailed guidelines for describing models and in silico experiments.

The importance of clear, concise and helpful documentation is paramount to ensuring a published model and results can be replicated independently of the original model implementation. It can be hard to write good prose and to teach the user rather than simply telling them what to do. Explanations can be confusing and difficult to understand. That's why it's important a have good editor; only edit the documentation yourself as a last resort. Good documentation means that your model/software is learnable.