R4EPIs project

RECON and MSF partnership

Waiting area for men in the shadow of a tree and an MSF car.

The waiting area for men in the shadow of a tree and an MSF car. 75-year-old Hassan (right), one of the community leaders in Ton-Habalan is waiting for his turn. Source: Susanne Doettling/MSF, 2019.

R4epis - what is it?

R4epis is a project to develop standardised data cleaning, analysis and reporting tools to cover common types of outbreaks and population-based surveys that would be conducted in an MSF emergency response setting.

This has been done through the development of the package sitrep in R software. The package provides field epidemiologists with novel data management tools as well as templates of automated “situation reports” that cover outbreak investigations (acute jaundice syndrome, cholera, measles, meningitis) and three of the MSF ERB pre-approved surveys (mortality, nutrition and vaccination).

All of the report templates are contained within the sitrep package as RMarkdown templates that can easily be used from within RStudio. The user then modifies a template to his/her needs.

The templates address all aspects of:

  • Data cleaning of outbreak linelists and survey data
  • Analysis of data to report in terms of time, place, and person
  • Analysis of survey data

All of the code is open source and freely available and can be used by anyone. For suggestions on what to add or change, please open an issue on GitHub. or contact one of our contributors.

Below: The “sitrep” package developed by R4Epis includes templates of automated situation reports Available situation report RMarkdown templates

Below: Report contents, including graphics and maps, can be modified with new data cleaning and analysis functions Data visualisation output

What is on this website?

This website provides support to users of sitrep with:

Who funded R4epis?

R4epis was funded through the Sapling Nursery, an MSF internal innovation fund for new projects that aim to improve the medical care MSF provides.

Who contributed to R4epis

R4epis has been a collaboration between the R for Epidemics Consortium (RECON) and MSF.

The project has merged the skills and experience of people in coding in R software, field epidemiology, spatial epidemiology, health information systems and public health.

Check out the list of project contributors.