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Wednesday, June 29 • 11:06am - 11:24am
On the emergence of R as a platform for emergency outbreak response

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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.

avatar for Karthik Ram

Karthik Ram

co-founder, rOpenSci
Karthik Ram is a co-founder of ROpenSci, and a data science fellow at the University of California's Berkeley Institute for Data Science. Karthik primarily works on a project that develops R-based tools to facilitate open science and access to open data.

avatar for Thibaut  Jombart

Thibaut Jombart

Lecturer, Imperial College London
About me ------------- Biostatistician working on disease outbreak response, pathogen population genetics, phylogenetics, and some random other things; R developer of adegenet, adephylo, apex, bmmix, dibbler, geoGraph, outbreaker(2), treescape, vimes, and a few more shameful projects... Read More →

Wednesday June 29, 2016 11:06am - 11:24am PDT
McCaw Hall