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https://github.com/epiverse-trace/episoap
[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
https://github.com/epiverse-trace/episoap
automated-report decision-support epidemiology epiverse literate-programming outbreak-analysis pipelines r r-package rmarkdown-templates
Last synced: about 1 month ago
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[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
- Host: GitHub
- URL: https://github.com/epiverse-trace/episoap
- Owner: epiverse-trace
- License: other
- Created: 2022-09-26T13:53:50.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-04-12T12:06:22.000Z (9 months ago)
- Last Synced: 2024-04-12T23:37:36.352Z (9 months ago)
- Topics: automated-report, decision-support, epidemiology, epiverse, literate-programming, outbreak-analysis, pipelines, r, r-package, rmarkdown-templates
- Language: R
- Homepage: https://epiverse-trace.github.io/episoap/
- Size: 11.5 MB
- Stars: 4
- Watchers: 3
- Forks: 2
- Open Issues: 42
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{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 
[](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)
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.