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https://github.com/epinowcast/epinowcast

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment
https://github.com/epinowcast/epinowcast

cmdstanr effective-reproduction-number-estimation epidemiology infectious-disease-surveillance nowcasting outbreak-analysis pandemic-preparedness real-time-infectious-disease-modelling stan

Last synced: 4 months ago
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A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment

Awesome Lists containing this project

README 

          
---

output: github_document

---



```{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

)

```

# A Bayesian Framework for Real-time Infectious Disease Surveillance epinowcast website



[![Lifecycle:

stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

[![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)



[![Universe](https://epinowcast.r-universe.dev/badges/epinowcast)](https://epinowcast.r-universe.dev/epinowcast)

[![MIT

license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epinowcast/blob/master/LICENSE.md/)

[![GitHub contributors](https://img.shields.io/github/contributors/epinowcast/epinowcast)](https://github.com/epinowcast/epinowcast/graphs/contributors)



[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)



## Summary



```{r, results = "asis", echo=FALSE}

cat(gsub("\n[ ]+", " ", packageDescription("epinowcast")$Description))

```



## Important Note on Model Specification



**The default lognormal reporting delay distribution may not suit all data.**

It can fail with multimodal or complex delay patterns.

Evaluate model fit and consider alternatives (e.g., non-parametric hazards) as needed.

See the [package vignettes](https://package.epinowcast.org/articles) for guidance.



## Installation

  

Installing the package



```{r, child="vignettes/chunks/_readme-install-epinowcast.Rmd"}

```



*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

`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 `epinowcast`, 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()

```



*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.*



Alternative: Docker



We 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.



## Resources



As 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:



Package Website



The [`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/).



R Vignettes



We have created [package vignettes](https://package.epinowcast.org/articles)

to help you

[get started nowcasting](https://package.epinowcast.org/articles/epinowcast.html),

see a

[quick reference to package capabilities](https://package.epinowcast.org/articles/features.html)

(different timesteps, multi-stratification, mixed models, etc.),

and

[explore case studies](https://package.epinowcast.org/articles/germany-age-stratified-nowcasting.html).



Organisation Website



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.



Community Forum



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 do not use `epinowcast`.



Package Analysis Scripts



In 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:



```{r, eval = FALSE}

list.files(

  system.file("examples", package = "epinowcast"), full.names = TRUE

)

```



## Contributing



We 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.



If 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.



### 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/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.



### Code of Conduct

  

Please 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.



## 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://package.epinowcast.org/articles/model.html). If you use `epinowcast` in your work, please consider citing it with `citation("epinowcast")`.



## Contributors



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



seabbs, 

adrian-lison, 

sbfnk, 

Bisaloo, 

pearsonca, 

choi-hannah, 

medewitt, 

jamesmbaazam, 

pitmonticone, 

athowes, 

jessalynnsebastian, 

kathsherratt, 

barbora-sobolova, 

kaitejohnson, 

Lnrivas, 

natemcintosh, 

nikosbosse, 

pratikunterwegs



### Issue Authors



teojcryan, 

FelixGuenther, 

beansrowning, 

jbracher, 

zsusswein, 

christinesangphet, 

rumackaaron, 

micahwiesner67, 

kylieainslie, 

maria-tang



### Issue Contributors



jhellewell14, 

Gulfa, 

parksw3, 

TimTaylor, 

WardBrian, 

jimrothstein