Pre-conference Workshop

The pre-conference workshop is now sold out.

Outbreak analysis using R: An introduction to new tools

Tuesday 28 November 2017 | 13.00 – 17.30

Leaders: Thibaut Jombart and Anne Cori, Imperial College London, UK


Outbreak analysis can be a complex task, involving a variety of analyses ranging from incidence computation and modelling, contact network analysis, estimation of key delays (e.g. incubation, serial interval), and increasingly frequent whole genome sequences (WGS) of pathogens. The R Epidemics Consortium (RECON: aims to provide efficient and reliable tools for such analyses using the free, open-source software R. This short course will provide an introduction to new RECON packages.

The first half of the course will be dedicated to outbreak response tools, based on the actual analyses run by the WHO Ebola response team during the West-African Ebola outbreak. These analyses will include the computation and visualisation of overall and stratified incidence, the estimation of doubling and halving times, the calibration of various delay distributions, the analysis of contact (exposure) data, and the estimation of reproduction numbers. The second half of the course will be devoted to the reconstruction of transmission chains from densely sampled outbreaks using WGS data. This will include the use of phylogenetic trees, and an introduction to the new package outbreaker2, which provides a flexible framework for outbreak reconstruction.

The workshop is open to EPIDEMICS 6 delegates only and is limited to 30 people.

The cost is €75.00  + taxes @ 21% = €90.75.  Please book via the online conference registration system.

The pre-conference workshop is now sold out.