From ff68bdba957ebb5fb8f5d642965d2fbc6775cc99 Mon Sep 17 00:00:00 2001
From: seabbs <20317649+seabbs@users.noreply.github.com>
Date: Mon, 25 Nov 2024 12:00:13 +0000
Subject: [PATCH] Automatic README update
---
README.md | 80 +++++++++++++++++++++++++++----------------------------
1 file changed, 40 insertions(+), 40 deletions(-)
diff --git a/README.md b/README.md
index b205ca575..09e74bf1f 100644
--- a/README.md
+++ b/README.md
@@ -33,19 +33,20 @@ 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
-
-Installing the package
+
+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:
@@ -59,7 +60,7 @@ install.packages(
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
+from Github (warning! this version may contain breaking changes and/or
bugs):
``` r
@@ -86,10 +87,10 @@ 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
@@ -123,8 +124,9 @@ 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),
@@ -132,10 +134,10 @@ 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)
@@ -148,7 +150,7 @@ 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
@@ -182,24 +184,26 @@ 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:
- Park S, Sam Abbott, Adam Howes (NULL). _epidist: Estimate
- epidemiological delay distributions for infectious diseases_.
- doi:10.5281/zenodo.5637165 .
+ Adam Howes, Park S, Sam Abbott (NULL). _epidist: Estimate
+ Epidemiological Delay Distributions With brms_.
+ doi:10.5281/zenodo.14213017
+ .
A BibTeX entry for LaTeX users is
@Manual{,
- title = {epidist: Estimate epidemiological delay distributions for infectious diseases},
- author = {Sang Woo Park and {Sam Abbott} and {Adam Howes}},
+ title = {epidist: Estimate Epidemiological Delay Distributions With brms},
+ author = {{Adam Howes} and Sang Woo Park and {Sam Abbott}},
year = {NULL},
- doi = {10.5281/zenodo.5637165},
+ doi = {10.5281/zenodo.14213017},
}
```
@@ -208,28 +212,26 @@ 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
@@ -253,7 +255,5 @@ Contributions of any kind are welcome\!
zsusswein
-
-