This package provides a store of curated outbreak analytics pipelines as rmarkdown reports.
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.
You can install the development version of soap from GitHub with:
# install.packages("devtools")
devtools::install_github("epiverse-trace/episoap")
Reports are provided a rmarkdown templates. You can load them either via RStudio graphical interface
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"
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.