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README.Rmd
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---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = file.path("man", "figures", "README-"),
out.width = "100%",
dpi = 330,
message = FALSE, warning = FALSE
)
```
# Estimate epidemiological delay distributions with `brms`<a href='https://epidist.epinowcast.org'><img src='man/figures/logo.png' align="right" height="139" /></a>
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/epinowcast/epidist)
[](https://epinowcast.r-universe.dev/epidist)
[](https://github.com/epinowcast/epidist/blob/master/LICENSE.md/)
[](https://github.com/epinowcast/epidist/graphs/contributors)
[](https://doi.org/10.5281/zenodo.14213017)
<!-- badges: end -->
## Summary
```{r, results = "asis", echo=FALSE}
cat(gsub("\n[ ]+", " ", packageDescription("epidist")$Description))
```
## Quickstart
To learn more about `epidist` we recommend reading the vignettes in this order:
* [Getting started with `epidist`](https://epidist.epinowcast.org/articles/epidist.html)
* [Using `epidist` to estimate delay between symptom onset and positive test for an Ebola outbreak in Sierra Leone](https://epidist.epinowcast.org/articles/ebola.html)
* [Approximate Bayesian inference in `epidist`](https://epidist.epinowcast.org/articles/approx-inference.html)
## Installation
<details><summary>Installing the package</summary>
You can install the latest released version using the normal `R` function, though you need to point to `r-universe` instead of CRAN:
```{r, eval = FALSE}
install.packages(
"epidist",
repos = "https://epinowcast.r-universe.dev"
)
```
Alternatively, you can use the [`remotes` package](https://remotes.r-lib.org/) to install the development version from Github (warning! this version may contain breaking changes and/or bugs):
```{r, eval = FALSE}
remotes::install_github(
file.path("epinowcast", "epidist"),
dependencies = TRUE
)
```
Similarly, you can install historical versions by specifying the release tag (e.g. this installs [`0.1.0`](https://github.com/epinowcast/epidist/releases/tag/v0.1.0)):
```{r, eval = FALSE}
remotes::install_github(
file.path("epinowcast", "epidist"),
dependencies = TRUE, ref = "v0.1.0"
)
```
*Note: You can also use that last approach to install a specific commit if needed, e.g. if you want to try out a specific unreleased feature, but not the absolute latest developmental version.*
</details>
<details><summary>Installing CmdStan (optional)</summary>
By default `epidist` uses the `rstan` package for fitting models. If you wish to use the `cmdstanr` package instead, you will need to install [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also entails having a suitable C++ toolchain setup. We recommend using the [`cmdstanr` package](https://mc-stan.org/cmdstanr/) to manage CmdStan. The Stan team provides instructions in the [_Getting started with
`cmdstanr`_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) vignette, with other details and support at the [package site](https://mc-stan.org/cmdstanr/), but the brief version is:
```{r, eval = FALSE}
# if you have not yet installed `epidist`, or you installed it without
# `Suggests` dependencies
install.packages(
"cmdstanr",
repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
)
# once `cmdstanr` is installed
cmdstanr::install_cmdstan()
```
*Note: You can speed up CmdStan installation using the `cores` argument. If you are installing a particular version of `epidist`, you may also need to install a past version of CmdStan, which you can do with the `version` argument.*
</details>
## Resources
<details><summary>Organisation Website</summary>
Our [organisation website](https://www.epinowcast.org/) includes links to other resources, [guest posts](https://www.epinowcast.org/blog.html), and [seminar schedule](https://www.epinowcast.org/seminars.html) for both upcoming and past recordings.
</details>
<details><summary>Community Forum</summary>
Our [community forum](https://community.epinowcast.org/) has areas for [question and answer](https://community.epinowcast.org/c/interface/15) and [considering new methods and tools](https://community.epinowcast.org/c/projects/11), among others. If you are generally interested in real-time analysis of infectious disease, you may find this useful even if do not use `epidist`.
</details>
## Contributing
We welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/epidist/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/epidist/pulls) and see our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.
### How to make a bug report or feature request
Please briefly describe your problem and what output you expect in an [issue](https://github.com/epinowcast/epidist/issues).
If you have a question, please don't open an issue. Instead, ask on our [forum](https://community.epinowcast.org/).
See our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.
### Code of Conduct
Please note that the `epidist` project is released with a [Contributor Code of Conduct](https://github.com/epinowcast/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
## Citation
If you use `epidist` in your work, please consider citing it using `citation("epidist")`.
<details><summary>Package citation information</summary>
```{r}
citation("epidist")
```
</details>
If using our methodology, or the methodology on which ours is based, please cite the relevant papers.
This may include:
* [Estimating epidemiological delay distributions for infectious diseases](https://www.medrxiv.org/content/10.1101/2024.01.12.24301247v1) by Park *et al.* (2024)
* [Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012520) by Charniga *et al.* (2024)
## Contributors
<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
<!-- prettier-ignore-start -->
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All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
### Code
<a href="https://github.com/epinowcast/epidist/commits?author=seabbs">seabbs</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=athowes">athowes</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=parksw3">parksw3</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=damonbayer">damonbayer</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=medewitt">medewitt</a>
### Issue Authors
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Akgostic">kgostic</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3ATimTaylor">TimTaylor</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Ajamesmbaazam">jamesmbaazam</a>
### Issue Contributors
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Apearsonca">pearsonca</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Asbfnk">sbfnk</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3ASamuelBrand1">SamuelBrand1</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Azsusswein">zsusswein</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Akcharniga">kcharniga</a>
<!-- markdownlint-enable -->
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<!-- ALL-CONTRIBUTORS-LIST:END -->