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

…#472) * fix badges, add R universe install, fix doi, fix commented epinowcast community code * adds a news item * update readme path handling * make links explicit
epinowcast · Nov 25, 2024 · b3d1905 · b3d1905
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diff --git a/NEWS.md b/NEWS.md
@@ -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.

diff --git a/README.Rmd b/README.Rmd
@@ -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
@@ -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(
@@ -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>
 
@@ -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
@@ -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
 

diff --git a/README.md b/README.md
@@ -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
@@ -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(
@@ -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
@@ -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
@@ -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)
@@ -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},
   }
@@ -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
 
@@ -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 -->
diff --git a/inst/CITATION b/inst/CITATION
@@ -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"
 )