This package provides a store of curated outbreak analytics pipelines as rmarkdown reports.

Target audience

The analyses are largely automated, and should be of use to any outbreak analyst. A basic R literacy will be required to adapt the report to other datasets.

Installation

You can install the development version of soap from GitHub with:

# install.packages("devtools")
devtools::install_github("epiverse-trace/episoap")

Usage

Reports are provided a rmarkdown templates. You can load them either via RStudio graphical interface

Graphical interface to open a soap rmarkdown template in RStudio

or by running:

rmarkdown::draft(file = "myreport.Rmd", template = "transmissibility", package = "episoap")

To get a list of the template reports available in this package, you can run:

episoap::list_templates()
#> [1] "transmissibility"

System dependencies

You may need to install system dependencies:

# macOS
brew install libsodium cmake

# Linux (Debian based)
apt install libsodium-dev cmake

This project has some overlap with other R packages:

  • {sitrep} from the Applied Epi organisation. While the stated goals and approaches can appear similar, episoap and {sitrep} are actually two very different projects. The {sitrep} reports are more specific (providing, e.g., reports for a specific disease although a generic template is in development), and thus more detailed. They are also more opinionated in the sense that they provide a single analysis path for each situation, based on the extensive experience of MSF. episoap on the other hand offers a more generic approach, with the emphasis on alternative paths you can take within a single analysis.

Acknowledgements

  • Thanks to Sam Abbott for pointing out issues with the way EpiNow2 was used in the transmissibility pipeline (#35)
  • The package logo is a derivative from a pipeline logo, provided by flaticon user “Eucalyp” for free for personal and commercial use with attribution.