Model fitting and inference for infectious disease dynamics
Introduction to the course and the instructors
Why this course?
Fitting a mechanistic model to data is a common task in an research on infectious disease dynamics.
The methods are often buried in the statistical literature, with little guidance on which particularapproach one should use.
There was no single place that taught them together.
The history
Taught at LSHTM for over a decade, by the Centre for the Mathematical Modelling of Infectious Diseases.
Written by Anton Camacho and Sebastian Funk, and developed since by several people.
It used R and a course-only package, which we told people never to use for real work.
This year it is Julia (bear with us), which can express every method we teach.
Who are we?
Who are you?
Around the room:
- your name
- where you have come from
- what you would like to fit a model to
How the course works
Each session opens with a short set of slides and then becomes a practical you work through.
The practicals are the course. Sit with someone and compare answers, and ask us as soon as you are stuck.
Every line of Julia is given complete. The exercises ask you to predict, interpret and choose, never to debug.
Your Turn
Head to
mfiidd.github.io
and click Getting Started to set your laptop up.
We are coming round, so put your hand up as soon as anything does not work.
Introduction to the course