Epidemics Analysis, Modelling and Response

Short Course, Bogota, 11-15 December 2017

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The course will be hosted at the Universidad Nacional de Colombia, Bogota. The exact location will be confirmed closer to the event.

Here is a map of the campus:

The course will take place over 5 days, 11-15 December 2017

Please use the google form below to register. Deadline for registration is 31st October 2017.

To register for the short course, you need to send your application the google form below [full page]:


If you would like to register for the course, please go to the 'register' section and use the form provided. To ask questions about the course, use the contacts provided below.

If you need financial support for travel and accommodation to attend the course, you can apply to a scholarship for this course. See the relevant section in the registration form (see 'register' section).

Content of the course

The course will provide an introduction to modelling and statistical techniques for analysing infectious disease epidemics. The methods presented will include tools for visualising epicurves, estimating transmissibility, deriving short term predictions of incidence, modelling infectious disease dynamics and assessing the impact of intervention strategies. The course will consist of lectures during the mornings and hands-on practical in the afternoon. All practicals will be using the R software. A basic knowledge of R will be assumed from the participants. The entirety of the course and teaching material will be in English. A certificate of attendance will be delivered upon completion of the course.

R refresher

Monday 11/12/2017 7:00 - Statistics Department UNAL, room 208

Practical introduction to R. Non-experienced R users are required to attend this session.



Opening seminar (public)

Monday 11/12/2017 10:00
Facluty of Science UNAL, Juan Herkrath auditorium

On the roles of statistics and modelling for informing outbreak response: examples from the West African Ebola outbreak and from the Zika epidemic.

Lecture 1

Monday 11/12/2017 13:00
Statistics Department UNAL, room 209

An introduction to infectious disease outbreak response: what data, what questions, and how to answer them?



Practical 1

Monday 11/12/2017 15:00
Statistics Department UNAL, room 208

Estimation of key delays, doubling time and transmissibility, short-term forecasting. R packages: incidence, distcrete, epitrix, EpiEstim, earlyR, projections

Lecture 2

Tuesday 12/12/2017 10:00
Statistics Department UNAL- room 209

Modelling epidemics using compartmental models 1: ‘simple’ models for directly transmitted diseases.

Practical 2

Tuesday 12/12/2017 13:00
Statistics Department UNAL- room 208

Modelling an Ebola outbreak and the impact of control strategies. R packages: odin, DeSolve



Lecture 3

Wednesday 13/12/2017 10:00
Statistics Department UNAL- room 209

Modelling epidemics using compartmental models 2: applications to vector-borne diseases.

Practical 3

Wednesday 13/12/2017 13:00
Statistics Department UNAL- room 208

Using compartmental models to model the spread of arboviruses. R packages: odin, DeSolve

Social event

Wednesday 13/12/2017 evening

Dinner with the participants. Venue and time will be confirmed closer to the event.




Lecture 4

Thursday 14/12/2017 10:00
Statistics Department UNAL- room 209

Using genetic sequences for inferring infectious disease dynamics.

Practical 4

Thursday 14/12/2017 13:00
Statistics Department UNAL- room 208

Introduction to phylogenetics, and disease outbreak reconstruction using epidemiological and genetic data. R packages: ape, phangorn, outbreaker2

Grant writing exercise

Friday 15/12/2017 10:00
Statistics Department UNAL- room 208

Participants will assemble into multidisciplinary teams, typically mixing public health officers, epidemiologists and methodologists, to formulate new projects in view of a grant application. The event will conclude with presentations of the projects and feedback from the panel.

Meet The Team

This short course is organised in collaboration between the National University of Colombia, Imperial College London, and the University of Sussex. Meet our teaching team below.

Liliana Lopez-Kleine

Professor, University Nacional de Colombia

Multivariate analysis, exploratory statistics, bioinformatics and system biology.

Thibaut Jombart

Lecturer, Imperial College London

Genetic epidemiology and outbreak response. Head of the R Epidemics Consortium (RECON).

Pierre Nouvellet

Reader, University of Sussex

Infectious disease modelling and outbreak response, with emphasis in zoonosis and emerging threats.

Zulma Cucunubá

Research Associate, Imperial College London

Modelling tropical disease dynamics and interventions. Member of the Vaccine Impact Modelling Consortium.

James Hayward

Senior Administrator, Imperial College London

Head administrator for the NIHR-HPRU, and logistics guru for the short course.