Introduction into R for surveillance and outbreak analytics

/// Short course on surveillance and outbreak analytics in R organised by RECON and EAN
/// Sofia, Bulgaria, SoHo, 8-11 October 2018

The workshop will be hosted at SoHo co-working company, Sofia, Bulgaria

Here is a map of the location:

The event will take place accross four days, Monday the 8th till Thursday the 11th of October 2018, exact times will be announced closer to the event. Please note that responses for registration are currently delayed due to holidays, we will respond to your registration half-August.

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, Phylogenetic analyses in R, GIS, automated report generation.


This four-day short course, co-organised by the R Epidemics Consortium (RECON) and the EPIET Alumni Network (EAN), will provide an introduction to surveillance and outbreak analysis using the R software. It will take place at SoHo workspace in Sofia Bulgaria, 8-11 October 2018. Participants will get an introduction and overview of conducting epidemiological analyses in R and gain practical experience of new packages for outbreak analysis developed by RECON, including descriptive approaches (epicurves), single- and multi-variable analyses (in the context of outbreak investigations) and depending on partipant feedback phylogenetic analyses using R, 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).


Organising members and facilitators

Thibaut Jombart

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

Outbreak response analytics and head of RECON.

Amrish Baidjoe

Research Associate, outbreak consultant, Imperial College London, UK

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

Janetta Skarp

Postgraduate student, Imperial College London

Course Facilitator - Infectious disease modelling

Savina Stoitsova

Infectious Disease Epidemiologist, National Center of Infectious and Parasitic Diseases, Bulgaria

Instigator of this event and EPIET alumni

Lieke van Alphen

Molecular Medical Microbiologist, MUMC, NL

Providing logistics support on behalf of EAN, EAN treasurer

Claire Thomson

Administrative support, Imperial College London, UK

Providing logistics support on behalf of Imperial College