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 - -