Epidemiologist R Handbook

Date published
May, 2021
Last updated
11 May 2021


The Epidemiologist R Handbook is a free, open-access R reference manual for applied epidemiology and public health. Written by epidemiologists, for epidemiologists, the handbook includes sample R code and tutorials addressing a wide range of data management and visualization tasks with epidemiological examples. An offline version is available for use in settings with low internet connectivity.

The handbook begins with R fundamentals and proceeds through topics including: data cleaning and management; descriptive and analytical approaches to linelist, survey, survival, contact tracing, time series, and geospatial data; creation of dashboards and automation of reports; how to generate figures such as epidemic curves, transmission chains, demographic pyramids, and phylogenetic trees; and epidemic modeling. It also provides guidance for people looking to transition to R from other software such as SAS, Stata, SPSS, or Excel.

Our Field Epidemiology Training Program (FETP) Alumni learning survey identified Advanced Epidemiological Methods to be the top additional training needs for FETP alumni.

Access the handbook here. 
Download the offline version here.