Introduction to Outbreaks Analytics using R

Coronavirus notice and FAQ - short course
Coronavirus information

LSHTM is following the latest advice for the UK from Public Health England (PHE) on the coronavirus outbreak. Health and Safety of our students and staff is our top priority and, with that in mind, a decision not to deliver any face-to-face teaching until at least September 2020 has been taken.

Wherever possible, an alternative online provision is being developed and we will publish further information on our website as soon as it is available. Unfortunately, not all of our Short Courses can be delivered at a distance and will sadly be either cancelled or postponed. If this affects you directly, we will be in touch with options opened to you. 

Courses scheduled to run from September onwards are currently planned to be delivered as normal. However, the situation is developing rapidly, and you are therefore encouraged to regularly check the latest updates on the situation through reliable sources such as Public Health England. We would also strongly advise offer holders to book refundable tickets and accommodation as there is a chance that this may change. 

overview - Introduction to Outbreaks Analytics using R

Course dates: 2 - 6 November 2020

This course will provide the students with an in-depth, practical introduction to outbreak analytics, a new data science dedicated to informing the response to epidemics in real time. Essential aspects of the analysis of outbreak data will be covered, including fundamental principles of statistics, good coding practices, scientific reproducibility and report automation, estimation of key epidemiological delays, mortality and transmissibility, short term forecasting, and the analysis of genetic data to reconstruct transmission trees.

Teaching will rely on a mixture of lectures and hands-on practicals using the R software, and involve the analysis of both simulated and actual disease outbreaks.

Course objectives

Day 1

  • Introduction: on the emergence of outbreak analytics and its role in outbreak response
  • Lecture: introduction to the R software
  • Practical: setting up R, Rstudio, using the RECON deployer
  • Lecture: principles of reproducible data science
  • Practical: reproducibility using R

Day 2

  • Lecture: key statistical aspects of outbreak analytics
  • Lecture: statistical analysis of outbreaks; mortality, delay distributions, and simple incidence models
  • Practical: simulated Ebola outbreak response – data handling and visualisation

Day 3

  • Lecture: primer on infectious disease modelling, estimating transmissibility and case forecasting
  • Practical: simulated Ebola outbreak response - transmissibility and forecasting

Day 4

  • Lecture: primer on genetic data analysis for outbreak response
  • Lecture: reconstructing transmission trees using epidemiological and genetic data
  • Practical: simulated Ebola outbreak response – inferring who infected whom

Day 5

  • Lecture: advanced tools for reproducible data science
  • Practical: open data session, build-your-own automated reporting infrastructure

Who should apply?

This course is open to field epidemiologists, public health practitioners, data managers, statisticians, computer scientists, data scientists, modellers with an interest in infectious disease outbreak response.

Methods of assessment

Students will not be formally assessed. The course will be assessed using anonymous online forms, circulated.

How to apply
How to apply - introduction to outbreak analytics using R

Applying for this course


Please read LSHTM's Admissions policies prior to submitting your application.

Short courses - visas, accommodation, disclaimer


The student is responsible for obtaining any visa or other permissions to attend the course, and is encouraged to start the application process as early as possible as obtaining a visa for the UK can sometimes take a long time. The Short Courses team can provide supporting documentation if requested.

Accommodation and meals

A list of hotels located in the vicinity of LSHTM, along with further resources for short term accommodation, can be found on our accommodation pages. Tea and coffee will be provided during breaks. Lunch vouchers for the LSHTM canteen will also be available.

Evening meals are not catered for at LSHTM, however there is a large choice of restaurants, cafés and shops nearby.

Important information

Please note:

  • If you have been offered a place on the course you will not be able to register without bringing formal ID (Passport) and without having obtained the correct visa if required.
  • It is essential that you read the current visa requirements for short course students.
  • LSHTM may cancel courses two weeks before the first day of the course if numbers prove insufficient.  In those circumstances, course fees will be refunded.
  • LSHTM cannot accept responsibility for accommodation, travel and other losses incurred as a result of the course being cancelled.