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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# episoap: A Store of Outbreak Analytics Pipelines <img src="man/figures/logo.svg" align="right" width="120" />
<!-- badges: start -->
[](https://github.com/epiverse-trace/episoap/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/epiverse-trace/episoap?branch=main)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<!-- badges: end -->
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](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("epiverse-trace/episoap")
```
## Usage
Reports are provided a [rmarkdown templates](https://rstudio.github.io/rstudio-extensions/rmarkdown_templates.html). You can load them either via RStudio graphical interface
or by running:
```{r, eval = FALSE}
rmarkdown::draft(file = "myreport.Rmd", template = "transmissibility", package = "episoap")
```
To get a list of the template reports available in this package, you can run:
```{r}
episoap::list_templates()
```
### System dependencies
You may need to install system dependencies:
```
# macOS
brew install libsodium cmake
# Linux (Debian based)
apt install libsodium-dev cmake
```
## Related projects
This project has some overlap with other R packages:
- [`{sitrep}`](https://github.com/R4EPI/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](https://www.flaticon.com/free-icon/pipeline_2082696), provided by [flaticon user "Eucalyp"](https://www.flaticon.com/authors/eucalyp) for free for personal and commercial use with attribution.