user2016

The recent Ebola virus disease outbreak in West Africa has been a terrible reminder of the necessities of rapid evaluation and response to emerging infectious disease threats. For such response to be fully informed, complex epidemiological data including dates of symptom onsets, locations of the cases, hospitalisation, contact tracing information and pathogen genome sequences have to be analysed in near real time. Integrating all these data to inform Public Health response is a challenging task, which typically involves a variety of visualisation tools and statistical approaches. However, a unified platform for outbreak analysis has been lacking so far. Some recent collaborative efforts, including several international hackathons, have been made to address this issue. This talk will provide an overview of the current state of R as a platform for the analysis of disease outbreaks, with an emphasis on lessons learnt from a direct involvement with the recent Ebola outbreak response.