diff --git a/README.Rmd b/README.Rmd
index 563f9b1ed..6d9b2b98b 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -19,16 +19,14 @@ knitr::opts_chunk$set(
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/epinowcast/epidist)
-
[](https://epinowcast.r-universe.dev/epidist)
[](https://github.com/epinowcast/epidist/blob/master/LICENSE.md/)
[](https://github.com/epinowcast/epidist/graphs/contributors)
-
[](https://zenodo.org/badge/latestdoi/422611952)
-*Warning: This package is a prototype and is under active development. Breaking changes are likely.*
+*Warning! This package is a prototype and is under active development. Breaking changes are likely.*
## Summary
@@ -36,6 +34,14 @@ license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/
cat(gsub("\n[ ]+"," ",packageDescription("epidist")$Description))
```
+## Quickstart
+
+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)
+
## Installation
Installing the package
@@ -58,25 +64,25 @@ 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.*
+
Installing CmdStan
-If you wish to do model fitting and nowcasting, you will need to install [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also entails having a suitable C++ toolchain setup. We recommend using the [`cmdstanr` package](https://mc-stan.org/cmdstanr/). The Stan team provides instructions in the [_Getting started with
+If you wish to do model fitting, you will need to install [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also entails having a suitable C++ toolchain setup. We recommend using the [`cmdstanr` package](https://mc-stan.org/cmdstanr/). The Stan team provides instructions in the [_Getting started with
`cmdstanr`_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) vignette, with other details and support at the [package site](https://mc-stan.org/cmdstanr/), but the brief version is:
```{r, eval = FALSE}
-# if you not yet installed `epinowcast`, or you installed it without `Suggests` dependencies
+# if you not yet installed `epidist`, or you installed it without `Suggests` dependencies
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# once `cmdstanr` is installed:
cmdstanr::install_cmdstan()
@@ -125,12 +131,23 @@ We welcome contributions and new contributors! We particularly appreciate help o
## Citation
-If making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [model outline](https://epidist.epinowcast.org/articles/model.html). If you use `epidist` in your work, please consider citing it with `citation("epidist")`.
+If you use `epidist` in your work, please consider citing it using `citation("epidist")`.
-## Contributors
+Package citation information
+```{r}
+citation("epidist")
+```
+
+
@@ -56,27 +67,20 @@ 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(
- "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.*
-
+
+
+
+
+
+
+
Installing CmdStan
-If you wish to do model fitting and nowcasting, you will need to install
+If you wish to do model fitting, you will need to install
[CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also
entails having a suitable C++ toolchain setup. We recommend using the
[`cmdstanr` package](https://mc-stan.org/cmdstanr/). The Stan team
@@ -86,7 +90,7 @@ vignette, with other details and support at the [package
site](https://mc-stan.org/cmdstanr/), but the brief version is:
``` r
-# if you not yet installed `epinowcast`, or you installed it without `Suggests` dependencies
+# if you not yet installed `epidist`, or you installed it without `Suggests` dependencies
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# once `cmdstanr` is installed:
cmdstanr::install_cmdstan()
@@ -147,12 +151,45 @@ request](https://github.com/epinowcast/epidist/pulls).
## Citation
-If making use of our methodology or the methodology on which ours is
-based, please cite the relevant papers from our [model
-outline](https://epidist.epinowcast.org/articles/model.html). If you use
-`epidist` in your work, please consider citing it with
+If you use `epidist` in your work, please consider citing it using
`citation("epidist")`.
+
+
+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 for infectious diseases_.
+ doi:10.5281/zenodo.5637165 .
+
+A BibTeX entry for LaTeX users is
+
+ @Manual{,
+ title = {epidist: Estimate epidemiological delay distributions for infectious diseases},
+ author = {{Adam Howes} and Sang Woo Park and {Sam Abbott}},
+ year = {NULL},
+ doi = {10.5281/zenodo.5637165},
+ }
+```
+
+
+
+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://arxiv.org/abs/2405.08841) by Charniga *et
+ al.* (2024)
+
## Contributors