R4 epis

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.

For more information, click HERE.