diff --git a/NEWS.md b/NEWS.md
index c4ddb509c..2153d2507 100644
--- 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
index 08deb3de9..ffaeeeb84 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -19,11 +19,12 @@ knitr::opts_chunk$set(
[](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://zenodo.org/badge/latestdoi/422611952)
+[](https://doi.org/10.5281/zenodo.14213017)
## Summary
@@ -44,17 +45,16 @@ To learn more about `epidist` we recommend reading the vignettes in this order:
Installing the package
-
-
-
-
-
-
-
+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 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)): -->
-
-
-
-
-
+```{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.*
-
-Installing the package
-
-
-
-
-
-
-
-
-
-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):
+
+Installing the package
+
+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
+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.*
+
+
-
-Installing CmdStan (optional)
-
+
+Installing CmdStan (optional)
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
@@ -110,9 +123,8 @@ need to install a past version of CmdStan, which you can do with the
## Resources
-
-Organisation Website
-
+
+Organisation Website
Our [organisation website](https://www.epinowcast.org/) includes links
to other resources, [guest posts](https://www.epinowcast.org/blog.html),
@@ -120,10 +132,10 @@ and [seminar schedule](https://www.epinowcast.org/seminars.html) for
both upcoming and past recordings.
+
-
-Community Forum
-
+
+Community Forum
Our [community forum](https://community.epinowcast.org/) has areas for
[question and answer](https://community.epinowcast.org/c/interface/15)
@@ -136,19 +148,33 @@ 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).
-
-
-
-
-
-
-
+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
@@ -156,23 +182,22 @@ If you use `epidist` in your work, please consider citing it using
`citation("epidist")`.
-
-Package citation information
-
+
+Package citation information
``` 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 .
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 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!
zsusswein
+
+
diff --git a/inst/CITATION b/inst/CITATION
index 0529927a0..b98e7e393 100644
--- 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"
)