Epi + R: from basics to advanced tools

The R Epidemics Consortium (RECON) and the EPIET Alumni Network (EAN) are joining forces for the second year and are organizing two parallel mini-modules in Epidemiology and R software! The event is taking place two days before ESCAIDE 2019 in lovely Stockholm!

Course #1: Introduction to epidemiological analysis using R

Course #2: Advanced course: tools for emergency outbreak response

The course will include a mixture of lectures and hands-on practicals.

A more detailed programme will be communicated closer to the event.

For more information visit the courses' website.

Venue

European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden. The exact address will be confirmed closer to the event.

Date: 25-26 November 2019

Register
Visit the website!
Course #1 /// Introduction to epidemiological analysis using R

Outline

  • Level: accessible to R beginners; see pre-requisites on the registration page.
  • Capacity: 40 participants
  • Summary: an introduction to using R for epidemiological analysis.

Course content

The following topics will be covered:

  • introduction to R and Rstudio
  • reading data from common formats (text files, Excel spreadsheets)
  • introduction to graphics using ggplot2
  • good practices for data science
  • introduction to automated reports using rmarkdown
  • hands on practical: the Stegen case study

Learning outcomes will include:

  • understanding of R basics
  • ability to structure a project
  • use of RECON deployer
  • ability to import and export data
  • methods for fast data cleaning
  • building meaningful graphics
  • ability to use automated data analysis reports
  • ability to generate simple tables and summaries
  • basics statistics including risk ratios and Fisher’s exact test
  • ability to generate static, and interactive maps
  • R packages used: rio, ggplot2, rmarkdown, incidence, epitrix, dplyr, sf
Course #2 /// Advanced course: tools for emergency outbreak response

Outline

  • Level: aimed at regular/experienced R users; see pre-requisites.
  • Capacity: 20 participants
  • Summary: an introduction to new R tools for emergency outbreak response, currently used in the Ebola outbreak, DRC

Course content

The following topics will be covered:

  • good practices for data science
  • refresher on Rmarkdown and some advanced practices
  • introduction to the linelist package
  • introduction to the reportfactory
  • primer on statistics for outbreak response
  • estimating transmissibility from case data
  • incidence forecasting
  • practical: simulated Ebola outbreak response

Learning outcomes will include,/li:

  • use of RECON deployer
  • advanced customisation of rmarkdown reports
  • advanced data cleaning using dictionaries
  • efficient data handling using dplyr
  • consolidated good practices for data science
  • handling multiple automated reports simultaneously
  • understanding of some essential statistical concepts for outbreak response, including models used for predicting future dynamics of cases
  • ability to handle, visualise and analyse transmission chains
  • R packages used: rio, ggplot2, dplyr, rmarkdown, incidence, epitrix, linelist, reportfactory, earlyR, EpiEstim, projections

Pricing

The cost of the courses is broken down into registration and catering fees as follows:

  • RECON / EAN members: € 50
  • Students: € 60
  • Academic staff: € 120
  • Others: € 200

Any inquiry can be sent by email to Amrish Baidjoe by clicking on this link.

Visit the website!