Resources

This page contains a non-exhaustive list of resources for learning R with a focus on epidemiology in humanitarian settings.

Want to add some other resources? Suggestions and contributions are welcome! Please open an issue or get in touch.


R Programming

  • DataCamp — Introduction to R. Interactive and beginner-friendly introduction to R.

  • Posit Cloud Primers. Browser-based interactive R tutorials covering the basics through to data visualisation and iteration.

  • R for Data Science. A good introduction to the tidyverse, covering data import, transformation, visualisation, and communication.

  • Advanced R. Deep dive into R’s internals and programming patterns.


Focus: Epidemiology and Statistics

  • The Epidemiologist R Handbook. An excellent resource for applied epidemiology in R. Written with field epidemiologists in mind, it covers outbreak investigation, survey analysis, GIS mapping, automated reporting, and more. Available in multiple languages.

  • Introduction to R for Health Data Science. Focused on health data, includes survival analysis and logistic regression.

  • Statistical Inference via Data Science. Gentle introduction to statistical thinking with R and the tidyverse.

  • The MSF-Epicentre Github. Provides a number of publicly available packages tailored to the specific needs of of MSF epidemiologists.

  • {sitrep}. Developed by R4EPIs / MSF. Templates and functions for situation reports in outbreak and survey contexts.

  • R4EPIs Project. MSF & RECON initiative providing standardised R templates and tutorials for field epidemiology: outbreak investigation, mortality surveys, and vaccination coverage surveys.


Focus: Surveys and Needs Assessments

  • {srvyr}. Tidyverse-style analysis tools for complex survey data (cluster sampling, stratification, weights). Particularly useful for SMART nutrition surveys, mortality surveys, and other humanitarian assessments. This package is based off of {survey}.

  • Exploring Complex Survey Data Analysis Using R. A useful text providing an in depth look at using {srvyr} and {survey}


Focus: GIS & Mapping


Focus: Reporting & Reproducibility

  • Quarto — A rich text format well suited for reproducible and automated reporting. Quarto supports reports, websites, and even simple dashboards.