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Issue #132: Updates to README #387

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merged 11 commits into from
Oct 15, 2024
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Issue #132: Updates to README #387

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a0f50e4
We don't have released versions!
athowes Oct 14, 2024
97e43f0
Likewise need to remove this
athowes Oct 14, 2024
a6b2d2b
Add citation information
athowes Oct 14, 2024
a21580c
Add vignettes and CAUTION
athowes Oct 14, 2024
6147658
Better text
athowes Oct 14, 2024
1792dec
Render
athowes Oct 14, 2024
4eb2882
Revert warning and add quickstart section
athowes Oct 14, 2024
e0c0b89
Code fold citation
athowes Oct 14, 2024
5189ab5
Remove enforced breaks
athowes Oct 14, 2024
f920b2a
Merge branch 'main' into readme-links
athowes Oct 15, 2024
4cc02e1
Merge branch 'main' into readme-links
athowes Oct 15, 2024
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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)

Comment on lines +39 to +44
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Sorry to comment though already merged. You could signpost in the vignettes using a format similar to that used in finalsize

## 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
View file
Open in desktop
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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