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56 changes: 31 additions & 25 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -19,23 +19,29 @@ knitr::opts_chunk$set(
[![Lifecycle:
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
[![R-CMD-check](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epinowcast/epidist/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/epidist)
</br>
[![Universe](https://epinowcast.r-universe.dev/badges/epidist)](https://epinowcast.r-universe.dev/epidist)
[![MIT
license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epidist/blob/master/LICENSE.md/)
[![GitHub contributors](https://img.shields.io/github/contributors/epinowcast/epidist)](https://github.com/epinowcast/epidist/graphs/contributors)
</br>
[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)
<!-- badges: end -->

*Warning: This package is a prototype and is under active development. Breaking changes are likely.*
*Warning! This package is a prototype and is under active development. Breaking changes are likely.*

## 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>
Expand All @@ -58,25 +64,25 @@ remotes::install_github(
)
```

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)):
<!-- 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(
"epinowcast/epidist", dependencies = TRUE, ref = "v0.2.0"
)
```
<!-- ```{r, eval = FALSE} -->
<!-- remotes::install_github( -->
<!-- "epinowcast/epidist", dependencies = TRUE, ref = "v0.2.0" -->
<!-- ) -->
<!-- ``` -->

*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.*
<!-- *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</summary>

If you wish to do model fitting and nowcasting, 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/). The Stan team provides instructions in the [_Getting started with
If you wish to do model fitting, 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/). 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 not yet installed `epinowcast`, or you installed it without `Suggests` dependencies
# if you not yet installed `epidist`, or you installed it without `Suggests` dependencies
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# once `cmdstanr` is installed:
cmdstanr::install_cmdstan()
Expand Down Expand Up @@ -125,12 +131,23 @@ We welcome contributions and new contributors! We particularly appreciate help o

## Citation

If making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [model outline](https://epidist.epinowcast.org/articles/model.html). If you use `epidist` in your work, please consider citing it with `citation("epidist")`.
If you use `epidist` in your work, please consider citing it using `citation("epidist")`.

## Contributors
<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://arxiv.org/abs/2405.08841) by Charniga *et al.* (2024)

## Contributors

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
<!-- prettier-ignore-start -->
Expand All @@ -140,36 +157,25 @@ All contributions to this project are gratefully acknowledged using the [`allcon

### 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>


<!-- markdownlint-enable -->
<!-- prettier-ignore-end -->
<!-- ALL-CONTRIBUTORS-LIST:END -->



83 changes: 60 additions & 23 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,17 +8,15 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
[![R-CMD-check](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml)
[![Codecov test
coverage](https://codecov.io/gh/epinowcast/epidist/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/epidist)
</br>
[![Universe](https://epinowcast.r-universe.dev/badges/epidist)](https://epinowcast.r-universe.dev/epidist)
[![MIT
license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epidist/blob/master/LICENSE.md/)
[![GitHub
contributors](https://img.shields.io/github/contributors/epinowcast/epidist)](https://github.com/epinowcast/epidist/graphs/contributors)
</br>
[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)
<!-- badges: end -->

*Warning: This package is a prototype and is under active development.
*Warning! This package is a prototype and is under active development.
Breaking changes are likely.*

## Summary
Expand All @@ -32,6 +30,19 @@ truncation, interval censoring, and dynamical biases. Despite their
importance, these issues are frequently overlooked, often resulting in
biased conclusions.

## 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>
Expand All @@ -56,27 +67,20 @@ remotes::install_github(
)
```

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
remotes::install_github(
"epinowcast/epidist", dependencies = TRUE, ref = "v0.2.0"
)
```

*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.*

<!-- 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( -->
<!-- "epinowcast/epidist", dependencies = TRUE, ref = "v0.2.0" -->
<!-- ) -->
<!-- ``` -->
<!-- *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
</summary>

If you wish to do model fitting and nowcasting, you will need to install
If you wish to do model fitting, 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/). The Stan team
Expand All @@ -86,7 +90,7 @@ vignette, with other details and support at the [package
site](https://mc-stan.org/cmdstanr/), but the brief version is:

``` r
# if you not yet installed `epinowcast`, or you installed it without `Suggests` dependencies
# if you not yet installed `epidist`, or you installed it without `Suggests` dependencies
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# once `cmdstanr` is installed:
cmdstanr::install_cmdstan()
Expand Down Expand Up @@ -147,12 +151,45 @@ request](https://github.com/epinowcast/epidist/pulls).

## Citation

If making use of our methodology or the methodology on which ours is
based, please cite the relevant papers from our [model
outline](https://epidist.epinowcast.org/articles/model.html). If you use
`epidist` in your work, please consider citing it with
If you use `epidist` in your work, please consider citing it using
`citation("epidist")`.

<details>
<summary>
Package citation information
</summary>

``` r
citation("epidist")
To cite package 'epidist' in publications use:

Adam Howes, Park S, Sam Abbott (NULL). _epidist: Estimate
epidemiological delay distributions for infectious diseases_.
doi:10.5281/zenodo.5637165 <https://doi.org/10.5281/zenodo.5637165>.

A BibTeX entry for LaTeX users is

@Manual{,
title = {epidist: Estimate epidemiological delay distributions for infectious diseases},
author = {{Adam Howes} and Sang Woo Park and {Sam Abbott}},
year = {NULL},
doi = {10.5281/zenodo.5637165},
}
```

</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://arxiv.org/abs/2405.08841) by Charniga *et
al.* (2024)

## Contributors

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
Expand Down

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