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Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"\",\n  fig.path = file.path(\"man\", \"figures\", \"README-\"),\n  out.width = \"100%\",\n  dpi = 330,\n  message = FALSE, warning = FALSE\n)\n```\n# A Bayesian Framework for Real-time Infectious Disease Surveillance \u003ca href=\"https://package.epinowcast.org/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" alt=\"epinowcast website\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle:\nstable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![R-CMD-check](https://github.com/epinowcast/epinowcast/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/epinowcast/epinowcast/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epinowcast/epinowcast/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/epinowcast)\n\u003c/br\u003e\n[![Universe](https://epinowcast.r-universe.dev/badges/epinowcast)](https://epinowcast.r-universe.dev/epinowcast)\n[![MIT\nlicense](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epinowcast/blob/master/LICENSE.md/)\n[![GitHub contributors](https://img.shields.io/github/contributors/epinowcast/epinowcast)](https://github.com/epinowcast/epinowcast/graphs/contributors)\n\u003c/br\u003e\n[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)\n\u003c!-- badges: end --\u003e\n\n## Summary\n\n```{r, results = \"asis\", echo=FALSE}\ncat(gsub(\"\\n[ ]+\", \" \", packageDescription(\"epinowcast\")$Description))\n```\n\n## Important Note on Model Specification\n\n**The default lognormal reporting delay distribution may not suit all data.**\nIt can fail with multimodal or complex delay patterns.\nEvaluate model fit and consider alternatives (e.g., non-parametric hazards) as needed.\nSee the [package vignettes](https://package.epinowcast.org/articles) for guidance.\n\n## Installation\n  \n\u003cdetails\u003e\u003csummary\u003eInstalling the package\u003c/summary\u003e\n\n```{r, child=\"vignettes/chunks/_readme-install-epinowcast.Rmd\"}\n```\n\n*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.*\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eInstalling CmdStan\u003c/summary\u003e\n\nIf 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\n`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:\n\n```{r, eval = FALSE}\n# if you not yet installed `epinowcast`, or you installed it without `Suggests` dependencies\ninstall.packages(\"cmdstanr\", repos = c(\"https://mc-stan.org/r-packages/\", getOption(\"repos\")))\n# once `cmdstanr` is installed:\ncmdstanr::install_cmdstan()\n```\n\n*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.*\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eAlternative: Docker\u003c/summary\u003e\n\nWe also provide a [Docker](https://www.docker.com/get-started/) image with [`epinowcast` and all dependencies installed](https://github.com/orgs/epinowcast/packages/container/package/epinowcast). You can use this image to run `epinowcast` without installing dependencies.\n\n\u003c/details\u003e\n\n## Resources\n\nAs you use the package, the documentation available via `?enw_` should be your first stop for troubleshooting. We also provide a range of other documentation, case studies, and community spaces to ask (and answer!) questions:\n\n\u003cdetails\u003e\u003csummary\u003ePackage Website\u003c/summary\u003e\n\nThe [`epinowcast` website](https://package.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://package.epinowcast.org/dev/).\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eR Vignettes\u003c/summary\u003e\n\nWe have created [package vignettes](https://package.epinowcast.org/articles)\nto help you\n[get started nowcasting](https://package.epinowcast.org/articles/epinowcast.html),\nsee a\n[quick reference to package capabilities](https://package.epinowcast.org/articles/features.html)\n(different timesteps, multi-stratification, mixed models, etc.),\nand\n[explore case studies](https://package.epinowcast.org/articles/germany-age-stratified-nowcasting.html).\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eOrganisation Website\u003c/summary\u003e\n\nOur [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.\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eCommunity Forum\u003c/summary\u003e\n\nOur [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 do not use `epinowcast`.\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003ePackage Analysis Scripts\u003c/summary\u003e\n\nIn addition to the vignettes, the package also comes with [example analyses](https://github.com/epinowcast/epinowcast/tree/main/inst/examples). These are not as polished as the vignettes, but we typically explore new features with these and they may help you if you are using a development version. After installing `epinowcast`, you can find them via:\n\n```{r, eval = FALSE}\nlist.files(\n  system.file(\"examples\", package = \"epinowcast\"), full.names = TRUE\n)\n```\n\n\u003c/details\u003e\n\n## Contributing\n\nWe welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/epinowcast/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/epinowcast/pulls) and see our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.\n\nIf you need a different underlying model for your work: `epinowcast` lets you pass your own models! If you do try new model parameterisations 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, whether or not they are directed at the core `epinowcast` applications.\n\n### How to make a bug report or feature request\n\nPlease briefly describe your problem and what output you expect in an [issue](https://github.com/epinowcast/epinowcast/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/epinowcast/discussions/categories/q-a). See our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information.\n\n### Code of Conduct\n  \nPlease note that the `epinowcast` 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.\n\n## Citation\n\nIf making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [model outline](https://package.epinowcast.org/articles/model.html). If you use `epinowcast` in your work, please consider citing it with `citation(\"epinowcast\")`.\n\n## Contributors\n\n\n\n\n\n\n\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\nAll 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!\n\n### Code\n\n\n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=seabbs\"\u003eseabbs\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=adrian-lison\"\u003eadrian-lison\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=sbfnk\"\u003esbfnk\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=Bisaloo\"\u003eBisaloo\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=pearsonca\"\u003epearsonca\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=choi-hannah\"\u003echoi-hannah\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=medewitt\"\u003emedewitt\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=jamesmbaazam\"\u003ejamesmbaazam\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=pitmonticone\"\u003epitmonticone\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=athowes\"\u003eathowes\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=jessalynnsebastian\"\u003ejessalynnsebastian\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=kathsherratt\"\u003ekathsherratt\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=barbora-sobolova\"\u003ebarbora-sobolova\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=kaitejohnson\"\u003ekaitejohnson\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=Lnrivas\"\u003eLnrivas\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=natemcintosh\"\u003enatemcintosh\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=nikosbosse\"\u003enikosbosse\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/commits?author=pratikunterwegs\"\u003epratikunterwegs\u003c/a\u003e\n\n\n\n### Issue Authors\n\n\n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Ateojcryan\"\u003eteojcryan\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3AFelixGuenther\"\u003eFelixGuenther\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Abeansrowning\"\u003ebeansrowning\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Ajbracher\"\u003ejbracher\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Azsusswein\"\u003ezsusswein\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Achristinesangphet\"\u003echristinesangphet\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Arumackaaron\"\u003erumackaaron\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Amicahwiesner67\"\u003emicahwiesner67\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Akylieainslie\"\u003ekylieainslie\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+author%3Amaria-tang\"\u003emaria-tang\u003c/a\u003e\n\n\n\n### Issue Contributors\n\n\n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3Ajhellewell14\"\u003ejhellewell14\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3AGulfa\"\u003eGulfa\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3Aparksw3\"\u003eparksw3\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3ATimTaylor\"\u003eTimTaylor\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3AWardBrian\"\u003eWardBrian\u003c/a\u003e, \n\u003ca href=\"https://github.com/epinowcast/epinowcast/issues?q=is%3Aissue+commenter%3Ajimrothstein\"\u003ejimrothstein\u003c/a\u003e\n\n\n\u003c!-- markdownlint-enable --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepinowcast%2Fepinowcast","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepinowcast%2Fepinowcast","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepinowcast%2Fepinowcast/lists"}