Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Issue #464 and #177: Bring README into line with epinowcast standards #472

Merged
merged 4 commits into from
Nov 25, 2024
Merged

Issue #464 and #177: Bring README into line with epinowcast standards #472

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
fc0be8f
fix badges, add R universe install, fix doi, fix commented epinowcast…
seabbs Nov 24, 2024
3b3a6c1
adds a news item
seabbs Nov 24, 2024
54eb8ec
update readme path handling
seabbs Nov 24, 2024
fd9e4df
make links explicit
seabbs Nov 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,14 @@

Development version of `epidist`.

## Package

- Remove the default method for `epidist()`. See #473.

## Documentation

- Brings the README into line with `epinowcast` standards. See #467.

# epidist 0.1.0

This is the first minor release of `epidist` intended for early test users of the package.
Expand Down
52 changes: 26 additions & 26 deletions README.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,12 @@ 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)

[![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)
[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14213017.svg)](https://doi.org/10.5281/zenodo.14213017)
<!-- badges: end -->

## Summary
Expand All @@ -44,17 +45,16 @@ To learn more about `epidist` we recommend reading the vignettes in this order:

<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" -->
<!-- ) -->
<!-- ``` -->
You can install the latest released version using the normal `R` function, though you need to point to `r-universe` instead of CRAN:

<!-- Alternatively, y -->
```{r, eval = FALSE}
install.packages(
"epidist",
repos = "https://epinowcast.r-universe.dev"
)
```

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):
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(
Expand All @@ -63,15 +63,16 @@ 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(
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.* -->
*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>

Expand All @@ -85,7 +86,7 @@ By default `epidist` uses the `rstan` package for fitting models. If you wish to
# `Suggests` dependencies
install.packages(
"cmdstanr",
repos = c("https://mc-stan.org/r-packages/", getOption("repos"))
repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
)

# once `cmdstanr` is installed
Expand All @@ -112,20 +113,19 @@ Our [community forum](https://community.epinowcast.org/) has areas for [question

## 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).
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.

<!-- and see our [contributing guide](CONTRIBUTING.md) for more information. -->
### How to make a bug report or feature request

<!-- ### 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).

<!-- 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/).

<!-- If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/dist/discussions/categories/q-a). -->
<!-- See our [contributing guide](CONTRIBUTING.md) for more information. -->
See our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.

<!-- ### Code of Conduct -->
### Code of Conduct

<!-- Please note that the `epidist` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. -->
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

Expand Down
157 changes: 93 additions & 64 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,13 @@ 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)

[![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)
[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14213017.svg)](https://doi.org/10.5281/zenodo.14213017)
<!-- badges: end -->

## Summary
Expand All @@ -32,31 +33,34 @@ biased conclusions.
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)
- [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, y -->

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):

<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
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
remotes::install_github(
Expand All @@ -65,18 +69,27 @@ 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, 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.* -->
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(
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>

<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
Expand All @@ -93,7 +106,7 @@ site](https://mc-stan.org/cmdstanr/), but the brief version is:
# `Suggests` dependencies
install.packages(
"cmdstanr",
repos = c("https://mc-stan.org/r-packages/", getOption("repos"))
repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
)

# once `cmdstanr` is installed
Expand All @@ -110,20 +123,19 @@ need to install a past version of CmdStan, which you can do with the
## Resources

<details>
<summary>
Organisation Website
</summary>

<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>

<summary>Community Forum</summary>

Our [community forum](https://community.epinowcast.org/) has areas for
[question and answer](https://community.epinowcast.org/c/interface/15)
Expand All @@ -136,43 +148,56 @@ disease, you may find this useful even if do not use `epidist`.

## Contributing

We welcome contributions and new contributors! We particularly
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).
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).

<!-- and see our [contributing guide](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 [Q and A page](https://github.com/epinowcast/dist/discussions/categories/q-a). -->
<!-- See our [contributing guide](CONTRIBUTING.md) for more information. -->
<!-- ### Code of Conduct -->
<!-- Please note that the `epidist` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. -->
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>

<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 With brms_.
Park S, Sam Abbott, Adam Howes (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 With brms},
author = {{Adam Howes} and Sang Woo Park and {Sam Abbott}},
title = {epidist: Estimate epidemiological delay distributions for infectious diseases},
author = {Sang Woo Park and {Sam Abbott} and {Adam Howes}},
year = {NULL},
doi = {10.5281/zenodo.5637165},
}
Expand All @@ -183,26 +208,28 @@ A BibTeX entry for LaTeX users is
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)
- [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 -->

<!-- markdownlint-disable -->

All contributions to this project are gratefully acknowledged using the
[`allcontributors`
package](https://github.com/ropenscilabs/allcontributors) following the
[all-contributors](https://allcontributors.org) specification.
Contributions of any kind are welcome!
Contributions of any kind are welcome\!

### Code

Expand All @@ -226,5 +253,7 @@ Contributions of any kind are welcome!
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Azsusswein">zsusswein</a>

<!-- markdownlint-enable -->

<!-- prettier-ignore-end -->

<!-- ALL-CONTRIBUTORS-LIST:END -->
2 changes: 1 addition & 1 deletion inst/CITATION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,5 +13,5 @@ bibentry(
title = paste0(meta$Package, ": ", gsub("[[:space:]]+", " ", meta$Title)),
author = author,
year = format(meta$Date, "%Y"),
doi = "10.5281/zenodo.5637165"
doi = "10.5281/zenodo.14213017"
)
Loading