Workshop on the Endemic-Epidemic framework for infectious disease modelling

Where: LSHTM (LG81, Lucas Room, Keppel St, London, WC1E 7HT) + online on Zoom

Building map

Registration link:

In-person attendance

Online attendance

When: 23 March 2022, 9:30-16:30

Host: Centre for Mathematical Modelling of Infectious Diseases at the London School of Hygiene & Tropical Medicine


Spatio-temporal models are used extensively to describe infectious disease dynamics while accounting for spatial heterogeneity in transmission risk. The Endemic-Epidemic modelling framework is a class of spatio-temporal models used for analysing subnational case count data implemented in the R package surveillance. It is characterised by its flexibility and ease of use, and it can easily integrate various data streams. It has been used to analyse outbreak dynamics in a wide range of settings, and applied to various diseases (including COVID-19, dengue, measles, and foot and mouth disease). This day-long workshop will provide an overview of the objectives and scope of Endemic-Epidemic models through a hands-on tutorial, followed by several short presentations and discussion on recent applications and future extensions of the framework.


Introduction, tutorial and summary

Material for tutorial

The code for the tutorial part of the workshop can be found here in the “tutorial” folders. In order to participate in the tutorial you will need to have R installed on your computer and to install the surveillance and hhh4addon R packages. Instructions for how to do this can be found in the README here.


Short talks - session 1
Short talks - session 2


Final programme (all in London time)

Time   Presenter
9:30 Welcome  
9:35 Introduction Leonhard Held
10:00 R tutorial: using hhh4 Sebastian Meyer
Johannes Bracher
Maria Bekker-Nielsen Dunbar
12:30 Lunch break  
13:30 Short talks on applications Mathilde Grimée
Trang Nguyen
Claudio Fronterre
Johannes Bracher
14:30 Coffee  
15:00 Short talks on applications Alastair Munro
Alexis Robert
Emily Nightingale
Cici Bauer
16:00 Discussion / Outlook  
16:30 Closing