To explain some of the concepts and packages involved:

Of note, the R4Epis project has developed template R Markdown scripts for common outbreaks and surveys scenarios encountered at MSF project locations.

The page Dashboards with R Markdown explains how to format a R Markdown report as a dashboard.

The page Organizing routine reports demonstrates how to routinize your report production with auto-generated time-stamped folders.

Other pages in this handbook expand on this topic:

Such documents can be produced to update on a routine basis (e.g. daily surveillance reports) and/or run on subsets of data (e.g. reports for each jurisdiction). You can create an entire formatted document, including narrative text (can be dynamic to change based on your data), tables, figures, bullets/numbers, bibliographies, etc. It can generate static or interactive outputs, in Word, pdf, html, powerpoint, and other formats.Īn R Markdown script intersperces R code and text such that the script actually becomes your output document. R Markdown is a widely-used tool for creating automated, reproducible, and share-worthy outputs, such as reports. 46 Version control and collaboration with Git and Github.

33 Demographic pyramids and Likert-scales.19 Univariate and multivariable regression.

Macdown example