Introduction to outbreak analysis using R

/// Short course on outbreak analytics organised by RECON and EAN
/// Malta, Mater Dei Hospital, 19-20 November 2018

The workshop will be hosted at the Mater Dei Hospital, Malta

Here is a map of the location:

The event will take place accross two days, Monday the 19th - and Tuesday the 20th of November 2018, exact times will be announced closer to the event.

Registrations have now been closed, at current there is a waiting list. Check the RECON site for future events, or contact RECON if you are interest in organising an event with us

For more information, use the contact details provided below, for question regarding registration, e-mail EAN.


What is on the menu?

The final programme of the short course will be published on this website soon. Upon registration, applicants are asked for their preferences in terms of content out of: R basics, epidemic curves, estimation of transmissibility, short-term incidence forecasting, GIS, automated report generation.


This two-days short course, co-organised by the R Epidemics Consortium (RECON) and the EPIET Alumni Network (EAN), will provide an introduction to outbreak analysis using the R software. It will take place in the Mater Dei Hospital Malta, 19-20 November 2018, as a satellite event to the ESCAIDE conference. The workshop will be aimed at people currently undertaking, or having recently completed, a field-epidemiology training programme (FETP), with some interest in epidemics analysis using R. Participants will get an overview and gain practical experience of new packages for outbreak analysis developed by RECON, including descriptive approaches (epicurves), short-term forecasting, or automated sitrep generation. While the course will be pitched at a beginner level, we strongly recommend that participants revise R basics by completing the free introduction session provided on the Swirl R package. Applications should be sent using the providing form (see 'Register' tab above).

At the end of the conference, there will additionally be a hackfest focused on generating case-studies and automated sitreps from your own data. You can find details on that at


Organising members and facilitators

Thibaut Jombart

Associate Professor, London School of Hygiene and Tropical Medicine / Imperial College London, UK

Facilitator - Outbreak response analytics and head of RECON

Amrish Baidjoe

Research Associate, Operational Outbreak Consultant, Imperial College London, UK

Facilitator - Field epidemiologist/microbiologist and coordinator of RECON, president of the EPIET Alumni Network

Zhian Kamvar

Research Associate, Imperial College London, UK

Facilitator - R developer and population geneticist; core developer and trainer for RECON

Alex Spina

R-outbreak Analytics Consultant

Course Facilitator - #Rstats

Patrick Keating

Data Scientist at the London School of Hygiene and Tropical Medicine

Course Facilitator - Member of the UK-Public Health Rapid Response Team

Finlay Campbell

PhD Student, , Imperial College London, UK

Course Facilitator - Developing methods and tools for inferring transmission during outbreaks

Janetta Skarp

Postgraduate student, Imperial College London

Course Facilitator - Infectious disease modelling

Claire Thomson

Administrative support, Imperial College London, UK

Providing logistics support on behalf of Imperial College

Lieke van Alphen

Molecular Medical Microbiologist, MUMC, NL

Providing logistics support on behalf of EAN, EAN treasurer

Chris Barbara

Chairman of the Pathology Department, Mater Dei Hospital, Malta

Chris made it possible to host us at Malta