OMNI/RÉUNIS Course on One Health Modelling for Emerging Infectious Diseases - Material of Julien Arino

This is the web version of my course page for the OMNI/RÉUNIS Course on One Health Modelling for Emerging Infectious Diseases. It is used to access the presentation files in html format. To view files in other formats, to access the code, etc., click the View on GitHub button to access the repository content. You can also download the whole repository by clicking the buttons on the left. (You can of course clone the repo, but will have to do it from the GitHub version.)

For those who would be looking for more details about the modelling part, I have slides and videos for a course in English et en français (la version française est plus complète mais toutes les vidéos n’ont pas encore été enregistrées/the French version is more comprehensive but not all videos are recorded yet).

List of lectures

Part I - Introduction

1. Introduction to the course and to this week’s lectures. Very brief history of Mathematical Epidemiology. Slides/Video
2. Basic mathematical epidemiology. Slides/Video
3. Simulating models in ODE and CTMC. Using the R programming language. Slides/Video

Part I - Environmentally transmitted pathogens

1. Environmental transmission of bacterial, parasitic, viral and fungal pathogens. Introduction. Slides/Video
2. Models for environmentally transmitted pathogens. Slides/Video
3. Models for environmentally transmitted pathogens - Part deux - Simulation. Slides/Video
4. Identifying parameters and identifiability issues. Slides/Video

Part II - Livestock diseases

Note that for now, I am using the following to have the information easily accessible, none of the topics below have slides at a point where they can be downloaded. Links to slides and videos will be added when they become available.

1. Introduction to foot and mouth disease, avian influenza Slides/Video
2. Introduction to livestock modelling Slides/Video
3. Introduction to mathematical modelling of foot and mouth disease in livestock Slides/Video
4. Introduction to mathematical modelling of avian influenza in livestock Slides/Video
5. Extension of the livestock models to include livestock movement (markets, trading between farms, selling for meat processing). Also considerations on control in the spatial context. Slides/Video 1/Video 2/Video 3