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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = file.path("man", "figures", "README-"),
out.width = "100%",
dpi = 330,
message = FALSE, warning = FALSE
)
```
# Primary event censored distributions <a href="https://primarycensored.epinowcast.org/"><img src="man/figures/logo.png" align="right" height="139" alt="primarycensored website" /></a>
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/epinowcast/primarycensored/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/epinowcast/primarycensored)
[](https://epinowcast.r-universe.dev/primarycensored)
[](https://github.com/epinowcast/primarycensored/blob/master/LICENSE.md/)
[](https://cran.r-project.org/web/packages/primarycensored/index.html)
[](https://github.com/epinowcast/primarycensored/graphs/contributors)
[](https://zenodo.org/doi/10.5281/zenodo.13632838)
<!-- badges: end -->
## Summary
```{r, results = "asis", echo=FALSE}
cat(gsub("\n[ ]+", " ", packageDescription("primarycensored")$Description))
```
## Installation
<details><summary>Installing the package</summary>
```{r, child="vignettes/chunks/_readme-install-primarycensored.Rmd"}
```
</details>
<details><summary>Installing CmdStan (optional for Stan functionality)</summary>
If you wish to use the Stan functions, 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/) along with some key instructions available in the [Stan resources package vignette](https://package.epinowcast.org/articles/stan-help.html#toolchain), but the brief version is:
```{r, eval = FALSE}
# if you not yet installed `primarycensored`, or you installed it without
# `Suggests` dependencies
install.packages(
"cmdstanr",
repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
)
# once `cmdstanr` is installed:
cmdstanr::install_cmdstan()
```
*Note: You can speed up CmdStan installation using the `cores` argument. If you are installing a particular version of `epinowcast`, you may also need to install a past version of CmdStan, which you can do with the `version` argument.*
</details>
## Resources
We provide a range of other documentation, case studies, and community spaces to ask (and answer!) questions:
<details><summary>Package Website</summary>
The [`primarycensored` website](https://primarycensored.epinowcast.org/) includes a function reference, model outline, and case studies using the package. The site mainly concerns the release version, but you can also find documentation for [the latest development version](https://primarycensored.epinowcast.org/dev/).
</details>
<details><summary>Vignettes</summary>
We have created [package vignettes](https://primarycensored.epinowcast.org/articles/) to help you get started with primarycensored and to highlight other features with case studies.
</details>
<details><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>
Our [community forum](https://community.epinowcast.org/) has areas for [question and answer](https://community.epinowcast.org/c/interface/15) and [considering new methods and tools](https://community.epinowcast.org/c/projects/11), among others. If you are generally interested in real-time analysis of infectious disease, you may find this useful even if you do not use `primarycensored`.
</details>
## Contributing
We welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/primarycensored/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/primarycensored/pulls) and see our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.
If you need a different underlying model for your work: `primarycensored` provides a flexible framework for censored distributions in both R and Stan. If you implement new distributions or censoring mechanisms that expand the overall flexibility or improve the defaults, please let us know either here or on the [community forum](https://community.epinowcast.org/). We always like to hear about new use-cases and extensions to the package.
### 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/primarycensored/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/primarycensored/discussions/categories/q-a). See our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.
### Code of Conduct
Please note that the `primarycensored` 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 making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [methods outline](https://primarycensored.epinowcast.org/articles//primarycensored.html). If you use `primarycensored` in your work, please consider citing it with `citation("primarycensored")`.
## 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/ropensci/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
### Code
<a href="https://github.com/epinowcast/primarycensored/commits?author=seabbs">seabbs</a>,
<a href="https://github.com/epinowcast/primarycensored/commits?author=SamuelBrand1">SamuelBrand1</a>,
<a href="https://github.com/epinowcast/primarycensored/commits?author=sbfnk">sbfnk</a>,
<a href="https://github.com/epinowcast/primarycensored/commits?author=athowes">athowes</a>
### Issue Authors
<a href="https://github.com/epinowcast/primarycensored/issues?q=is%3Aissue+author%3Azsusswein">zsusswein</a>,
<a href="https://github.com/epinowcast/primarycensored/issues?q=is%3Aissue+author%3Ajcblemai">jcblemai</a>,
<a href="https://github.com/epinowcast/primarycensored/issues?q=is%3Aissue+author%3Ajamesmbaazam">jamesmbaazam</a>
### Issue Contributors
<a href="https://github.com/epinowcast/primarycensored/issues?q=is%3Aissue+commenter%3Aparksw3">parksw3</a>
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<!-- prettier-ignore-end -->
<!-- ALL-CONTRIBUTORS-LIST:END -->