Introduction to Outbreak Analytics using R

Online short course

overview - Introduction to Outbreaks Analytics using R

Course dates: 22 - 26 November 2021

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.

Due to the COVID-19 situation, all teaching will be done online, and involve a mixture of lectures, group discussions, and hands-on practical sessions using the R software. Worked examples will be based on direct experience of outbreak responses, including the Ebola epidemic in Eastern Democratic Republic of the Congo (2018 - 2020), and the response to COVID-19 in the UK. Lectures will be recorded and made available online to participants.

Read our student testimonials to hear about their experience of the course.    

Course objectives

Day 1

  • General introduction to the course
  • Lecture: on the emergence of outbreak analytics and its role in outbreak response
  • Group discussion: what are the key questions in early outbreak responses?
  • Practical: setting up R, Rstudio, using the RECON deployer
  • Lecture/practical: introduction to data handling and visualisation using dplyr and ggplot2
  • Lecture: principles of reproducible data science
  • Practical: reproducibility using R

Day 2

  • Lecture: a primer on key statistical concepts for outbreak response
  • Lecture: descriptive epidemiology; epidemic curves; estimating mortality; characterising delay distributions; analysing contact data
  • Practical: simulated Ebola outbreak response – data handling and visualisation

Day 3

  • Lecture: primer on infectious disease modelling; estimating transmissibility (reproduction numbers, growth rates, doubling time); short term forecasting
  • Practical: simulated Ebola outbreak response - transmissibility and forecasting; real-life application to publicly available COVID-19 data

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. A basic knowledge of R is encouraged, but the course will start at a beginner level.

Methods of assessment

Students will not be formally assessed. The course will be assessed using anonymous online forms, circulated. A Certificate of Attendance will be provided. 

Testimonials - Introduction to Outbreak Analytics using R short course

'Absolutely excellent! In my 10 years of student experience, this one was the best one.'

'The best online course I have attended so far, great balance between theory, group discussions, examples and practicals.'

'I've never seen stats and modelling taught as clearly as Thibaut does it. I'm so impressed with how well he filters out exactly what's needed for varied experience levels. '

'It was really useful and extremely good as they covered the topics for beginners to more experienced.'

'Excellent trainers, explained things clearly. They are very helpful, friendly and informative.'

'They took away my fear of coding on R and I am pretty confident I can figure other things I need on my own. The help files sent are also excellent and tailored towards my needs compared to random searches online. I'm going to be proficient with R and outbreak analytics. Thank you very much. '

'Fantastic teachers, really good online set-up, thorough practicals. '

'Excellent trainers, explained things clearly. They are very helpful, friendly and informative.'

'Covered a huge amount of info, which was fantastic.  Learned a lot more about R.'

'It was wonderful - so useful and I'm very eager to get started with this properly. I only wish I'd had more R knowledge at the start so will go through this AFTER doing a more basic R course.'

'Exceptional teaching, and it's been interesting to learn from other 'students' about their own experience. I've really enjoyed the collaborative, friendly structure (i.e. with time given to learn from the other students in small groups), especially having come from a very exclusionary academic research group.'

'Really good and in depth course - very well explaining also for beginners even though the material is quite tough.'

How to apply
How to apply - Outbreak Analytics using R short course

Applying for this course

Applications for 2021 are now closed. Register your interest to be notified when they reopen. 

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