epinow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

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Keywords

backcalculation covid-19 gaussian-processes open-source reproduction-number rstats stan

Keywords from Contributors

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

Last synced: 6 months ago · JSON representation ·

Repository

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

Basic Info

Host: GitHub
Owner: epiforecasts
License: other
Language: R
Default Branch: main
Homepage: https://epiforecasts.io/EpiNow2/dev/
Size: 103 MB

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Stars: 131
Watchers: 9
Forks: 38
Open Issues: 63
Releases: 18

Topics

backcalculation covid-19 gaussian-processes open-source reproduction-number rstats stan

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

README.Rmd

---
output: github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/", # nolint
  eval = TRUE
)
```

# EpiNow2: Estimate real-time case counts and time-varying epidemiological parameters 

[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing) [![R-CMD-check](https://github.com/epiforecasts/EpiNow2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiforecasts/EpiNow2/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/epiforecasts/EpiNow2/branch/main/graph/badge.svg?token=FZWwEMdpq6)](https://app.codecov.io/gh/epiforecasts/EpiNow2) [![](https://cranlogs.r-pkg.org/badges/grand-total/EpiNow2)](https://cran.r-project.org/package=EpiNow2)

[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/EpiNow2/blob/main/LICENSE.md/)   [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/EpiNow2)](https://github.com/epiforecasts/EpiNow2/graphs/contributors)  [![universe](https://epiforecasts.r-universe.dev/badges/EpiNow2)](http://epiforecasts.r-universe.dev/#package:EpiNow2) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/EpiNow2/v1.7.1.svg?color=orange)](https://GitHub.com/epiforecasts/EpiNow2/commit/main/) [![DOI](https://zenodo.org/badge/272995211.svg)](https://zenodo.org/badge/latestdoi/272995211)

## Summary

`{EpiNow2}` estimates the time-varying reproduction number, growth rate, and doubling time using a range of open-source tools ([Abbott et al.](https://doi.org/10.12688/wellcomeopenres.16006.1)), and current best practices ([Gostic et al.](https://doi.org/10.1371/journal.pcbi.1008409)). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.

Forecasting is also supported for the time-varying reproduction number, infections, and reported cases using the same generative process approach as used for estimation.

  More details 

`{EpiNow2}` estimates the time-varying reproduction number on cases by date of infection (using a similar approach to that implemented in [`{EpiEstim}`](https://github.com/mrc-ide/EpiEstim)). True infections, treated as latent and unobserved, are estimated and then mapped to observed data (for example cases by date of report) via one or more delay distributions (in the examples in the package documentation these are an incubation period and a reporting delay) and a reporting model that can include weekly periodicity. 

Uncertainty is propagated from all inputs into the final parameter estimates, helping to mitigate spurious findings. This is handled internally. The time-varying reproduction estimates and the uncertain generation time also give time-varying estimates of the rate of growth.



  Models provided 

`{EpiNow2}` provides three models:

* `estimate_infections()`: Reconstruct cases by date of infection from reported cases.

* `estimate_secondary()`: Estimate the relationship between primary and secondary observations, for example, deaths (secondary) based on hospital admissions (primary), or bed occupancy (secondary) based on hospital admissions (primary).

* `estimate_truncation()`: Estimate a truncation distribution from multiple snapshots of the same data source over time. For more flexibility, check out the [`{epinowcast}`](https://package.epinowcast.org/) package.


The default model in `estimate_infections()` uses a non-stationary Gaussian process to estimate the time-varying reproduction number and infer infections. Other options, which generally reduce runtimes at the cost of the granularity of estimates or real-time performance, include:

* A stationary Gaussian process (faster to estimate but currently gives reduced performance for real time estimates).
* User specified breakpoints.
* A fixed reproduction number.
* A piecewise constant, combining a fixed reproduction number with breakpoints.
* A random walk, combining a fixed reproduction number with regularly spaced breakpoints (i.e weekly).
* A deconvolution/back-calculation method for inferring infections, followed with calculating the time-varying reproduction number.
* Adjustment for the remaining susceptible population beyond the forecast horizon.

By default, all these models are fit with [MCMC sampling](https://mc-stan.org/docs/reference-manual/mcmc.html) using the [`rstan`](https://mc-stan.org/users/interfaces/rstan) R package as the backend. Users can, however, switch to use approximate algorithms like [variational inference](https://en.wikipedia.org/wiki/Variational_Bayesian_methods), the [pathfinder](https://mc-stan.org/docs/reference-manual/pathfinder.html) algorithm, or [Laplace approximation](https://mc-stan.org/docs/reference-manual/laplace.html) especially for quick prototyping. The latter two methods are provided through the [`cmdstanr`](https://mc-stan.org/cmdstanr/) R package, so users will have to install that separately.

The documentation for `estimate_infections` provides examples of the implementation of the different options available. 

`{EpiNow2}` is designed to be used via a single function call to two functions:

* `epinow()`: Estimate Rt and cases by date of infection and forecast these infections into the future.

* `regional_epinow()`: Efficiently run `epinow()` across multiple regions in an efficient manner.

These two functions call `estimate_infections()`, which works to reconstruct cases by date of infection from reported cases.

For more details on using each function corresponding function documentation.



## Installation

Install the released version of the package:

```{r, eval = FALSE}
install.packages("EpiNow2")
```

Install the development version of the package with:

```{r, eval = FALSE}
install.packages("EpiNow2", repos = c("https://epiforecasts.r-universe.dev", getOption("repos")))
```

Alternatively, install the development version of the package with [pak](https://pak.r-lib.org/)
as follows (few users should need to do this):

```{r, eval = FALSE}
# check whether {pak} is installed
if (!require("pak")) {
  install.packages("pak")
}
pak::pkg_install("epiforecasts/EpiNow2")
```

If using `pak` fails, try:
```{r, eval = FALSE}
# check whether {remotes} is installed
if (!require("remotes")) {
  install.packages("remotes")
}
remotes::install_github("epiforecasts/EpiNow2")
```

To build `{EpiNow2}` from source, users will need to configure their C toolchain. This is because `{EpiNow2}` implements the underlying models in Stan (a statistical modelling programming language), which is built on C++.

Each operating system has a different set up procedure. Windows users need to install an appropriate version of [RTools](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows). Mac users can [follow these steps](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac), and Linux users can use [this guide](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux).

## Resources

  Getting Started 

The Getting Started vignette (see `vignette("EpiNow2")`)
is your quickest entry point to the package. It provides a quick run through of
the two main functions in the package and how to set up them up. It also
discusses how to summarise and visualise the results after running the models.

More broadly, users can also learn the details of estimating delay distributions, nowcasting, and forecasting in a structured way through the free and open short-course, ["Nowcasting and forecasting infectious disease dynamics"](https://nfidd.github.io/nfidd/), developed by some authors of this package.



  Package website 

The package has two websites: one for
[the stable release version on CRAN](https://epiforecasts.io/EpiNow2/), and
another for [the version in development](https://epiforecasts.io/EpiNow2/dev/).
These two provide various resources for learning about the package, including
the function reference, details about each model (model definition), workflows
for each model (usage), and case studies or literature of applications of
the package. However, the development website may contain experimental features
and information not yet available in the stable release.



  End-to-end workflows 

The workflow vignette (see `vignette("estimate_infections_workflow")`)
provides guidance on the end-to-end process of estimating reproduction
numbers and performing short-term forecasts for a disease spreading in a



  Model definitions 

In different vignettes we provide the mathematical definition of each model.
For example, the model definition vignette for `estimate_infections()` can be
found in `vignette("estimate_infections")`.



  Example implementations 

A simple example of using the package to estimate a national Rt for Covid-19 can be found [here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867).



## Contributing

We welcome all contributions. If you have identified an issue with the package,
you can file an issue [here](https://github.com/epiforecasts/EpiNow2/issues). We also welcome additions and extensions to the underlying model either in the form of options or improvements. If you wish to contribute in any form, please follow the
[package contributing guide](https://github.com/epiforecasts/EpiNow2/blob/main/.github/CONTRIBUTING.md).

## Contributors














All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [allcontributors](https://allcontributors.org) specification. Contributions of any kind are welcome!

### Code


seabbs, 
sbfnk, 
jamesmbaazam, 
joeHickson, 
hsbadr, 
pitmonticone, 
actions-user, 
ellisp, 
kaitejohnson, 
jdmunday, 
pearsonca, 
Bisaloo, 
JAllen42, 
adamkucharski, 
avehtari, 
andrjohns, 
jcken95, 
LloydChapman, 
medewitt, 
nikosbosse, 
sophiemeakin, 
zsusswein



### Issue Authors


raulfernandezn, 
pcarbo, 
johnaponte, 
sophie-schiller, 
munozedg, 
kathsherratt, 
yungwai, 
kgostic, 
fkrauer, 
philturk, 
krageth, 
tony352, 
username-rp, 
HAKGH, 
AndrewRiceMGW, 
brynhayder, 
RichardMN, 
andrybicio, 
rhamoonga, 
furqan915, 
MFZaini1984, 
fabsig, 
affans, 
GauriSaran, 
davidvilanova, 
jrcpulliam, 
dajmcdon, 
joshwlambert, 
avallecam, 
athowes, 
lorenzwalthert, 
nlinton, 
martinamcm, 
adrian-lison, 
jonathonmellor, 
TimTaylor, 
ciaramccarthy1, 
SamuelBrand1, 
damonbayer



### Issue Contributors


jhellewell14, 
thlytras, 
LizaHadley, 
ntorresd, 
micahwiesner67, 
paigemiller

Owner

Name: Epiforecasts
Login: epiforecasts
Kind: organization
Email: sebastian.funk@lshtm.ac.uk
Location: London

Website: https://epiforecasts.io
Twitter: sbfnk
Repositories: 56
Profile: https://github.com/epiforecasts

Researchers at the London School of Hygiene & Tropical Medicine doing research to forecast infectious diseases and perform real-time analyses.

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "EpiNow2" in publications use:'
type: software
license: MIT
title: 'EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters'
version: 1.7.1.9000
doi: 10.32614/CRAN.package.EpiNow2
identifiers:
- type: url
  value: https://epiforecasts.io/EpiNow2/dev/
abstract: Estimates the time-varying reproduction number, rate of spread, and doubling
  time using a range of open-source tools (Abbott et al. (2020) <https://doi.org/10.12688/wellcomeopenres.16006.1>),
  and current best practices (Gostic et al. (2020) <https://doi.org/10.1101/2020.06.18.20134858>).
  It aims to help users avoid some of the limitations of naive implementations in
  a framework that is informed by community feedback and is actively supported.
authors:
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  given-names: Sam
  email: sam.abbott@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-8057-8037
- family-names: Hellewell
  given-names: Joel
  email: joel.hellewell@lshtm.ac.uk
  orcid: https://orcid.org/0000-0003-2683-0849
- family-names: Sherratt
  given-names: Katharine
  email: katharine.sherratt@lshtm.ac.uk
- family-names: Gostic
  given-names: Katelyn
  email: kgostic@uchicago.edu
- family-names: Hickson
  given-names: Joe
  email: joseph.hickson@metoffice.gov.uk
- family-names: Badr
  given-names: Hamada S.
  email: badr@jhu.edu
  orcid: https://orcid.org/0000-0002-9808-2344
- family-names: DeWitt
  given-names: Michael
  email: me.dewitt.jr@gmail.com
  orcid: https://orcid.org/0000-0001-8940-1967
- family-names: Azam
  given-names: James M.
  email: james.azam@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-5782-7330
- name: EpiForecasts
- family-names: Funk
  given-names: Sebastian
  email: sebastian.funk@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-2842-3406
repository: https://CRAN.R-project.org/package=EpiNow2
repository-code: https://github.com/epiforecasts/EpiNow2
url: https://epiforecasts.io/EpiNow2/
contact:
- family-names: Funk
  given-names: Sebastian
  email: sebastian.funk@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-2842-3406
keywords:
- backcalculation
- covid-19
- gaussian-processes
- open-source
- reproduction-number
- rstats
- stan
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  - family-names: Gabry
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    email: jsg2201@columbia.edu
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Johnson
    given-names: Andrew
    email: andrew.johnson@arjohnsonau.com
  - family-names: Weber
    given-names: Sebastian
    email: sdw.post@waebers.de
  - family-names: Badr
    given-names: Hamada S.
    email: badr@jhu.edu
    orcid: https://orcid.org/0000-0002-9808-2344
  year: '2025'
  doi: 10.32614/CRAN.package.rstan
  version: '>= 2.26.0'
- type: software
  title: rstantools
  abstract: 'rstantools: Tools for Developing R Packages Interfacing with ''Stan'''
  notes: Imports
  url: https://mc-stan.org/rstantools/
  repository: https://CRAN.R-project.org/package=rstantools
  authors:
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Lysy
    given-names: Martin
    email: mlysy@uwaterloo.ca
  - family-names: Johnson
    given-names: Andrew
  year: '2025'
  doi: 10.32614/CRAN.package.rstantools
  version: '>= 2.2.0'
- type: software
  title: runner
  abstract: 'runner: Running Operations for Vectors'
  notes: Imports
  url: https://github.com/gogonzo/runner
  repository: https://CRAN.R-project.org/package=runner
  authors:
  - family-names: Kałędkowski
    given-names: Dawid
    email: dawid.kaledkowski@gmail.com
    orcid: https://orcid.org/0000-0001-9533-457X
  year: '2025'
  doi: 10.32614/CRAN.package.runner
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2025'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: truncnorm
  abstract: 'truncnorm: Truncated Normal Distribution'
  notes: Imports
  url: https://github.com/olafmersmann/truncnorm
  repository: https://CRAN.R-project.org/package=truncnorm
  authors:
  - family-names: Mersmann
    given-names: Olaf
    email: olafm@p-value.net
  - family-names: Trautmann
    given-names: Heike
  - family-names: Steuer
    given-names: Detlef
  - family-names: Bornkamp
    given-names: Björn
  year: '2025'
  doi: 10.32614/CRAN.package.truncnorm
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: cmdstanr
  abstract: 'cmdstanr: R Interface to ''CmdStan'''
  notes: Suggests
  url: https://mc-stan.org/cmdstanr/
  authors:
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Češnovar
    given-names: Rok
    email: rok.cesnovar@fri.uni-lj.si
  - family-names: Johnson
    given-names: Andrew
    email: andrew.johnson@arjohnsonau.com
    orcid: https://orcid.org/0000-0001-7000-8065
  - family-names: Bronder
    given-names: Steve
  year: '2025'
- type: software
  title: future
  abstract: 'future: Unified Parallel and Distributed Processing in R for Everyone'
  notes: Suggests
  url: https://future.futureverse.org
  repository: https://CRAN.R-project.org/package=future
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
    orcid: https://orcid.org/0000-0002-7579-5165
  year: '2025'
  doi: 10.32614/CRAN.package.future
- type: software
  title: future.apply
  abstract: 'future.apply: Apply Function to Elements in Parallel using Futures'
  notes: Suggests
  url: https://future.apply.futureverse.org
  repository: https://CRAN.R-project.org/package=future.apply
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
    orcid: https://orcid.org/0000-0002-7579-5165
  year: '2025'
  doi: 10.32614/CRAN.package.future.apply
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr
- type: software
  title: BH
  abstract: 'BH: Boost C++ Header Files'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/bh.html
  repository: https://CRAN.R-project.org/package=BH
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Emerson
    given-names: John W.
  - family-names: Kane
    given-names: Michael J.
    orcid: https://orcid.org/0000-0003-1899-6662
  year: '2025'
  doi: 10.32614/CRAN.package.BH
  version: '>= 1.66.0'
- type: software
  title: RcppEigen
  abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra
    Library'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/rcpp.eigen.html
  repository: https://CRAN.R-project.org/package=RcppEigen
  authors:
  - family-names: Bates
    given-names: Doug
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Francois
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Qiu
    given-names: Yixuan
    orcid: https://orcid.org/0000-0003-0109-6692
  year: '2025'
  doi: 10.32614/CRAN.package.RcppEigen
  version: '>= 0.3.3.3.0'
- type: software
  title: RcppParallel
  abstract: 'RcppParallel: Parallel Programming Tools for ''Rcpp'''
  notes: LinkingTo
  url: https://rcppcore.github.io/RcppParallel/
  repository: https://CRAN.R-project.org/package=RcppParallel
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Francois
    given-names: Romain
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Vandenbrouck
    given-names: Gregory
  - family-names: Geelnard
    given-names: Marcus
    website: https://tinythreadpp.bitsnbites.eu/
  - name: Intel
    website: https://www.threadingbuildingblocks.org/
  year: '2025'
  doi: 10.32614/CRAN.package.RcppParallel
  version: '>= 5.0.1'
- type: software
  title: StanHeaders
  abstract: 'StanHeaders: C++ Header Files for Stan'
  notes: LinkingTo
  url: https://mc-stan.org/
  repository: https://CRAN.R-project.org/package=StanHeaders
  authors:
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Gelman
    given-names: Andrew
  - family-names: Carpenter
    given-names: Bob
  - family-names: Hoffman
    given-names: Matt
  - family-names: Lee
    given-names: Daniel
  - family-names: Betancourt
    given-names: Michael
  - family-names: Brubaker
    given-names: Marcus
  - family-names: Guo
    given-names: Jiqiang
  - family-names: Li
    given-names: Peter
  - family-names: Riddell
    given-names: Allen
  - family-names: Inacio
    given-names: Marco
  - family-names: Morris
    given-names: Mitzi
  - family-names: Arnold
    given-names: Jeffrey
  - family-names: Goedman
    given-names: Rob
  - family-names: Lau
    given-names: Brian
  - family-names: Trangucci
    given-names: Rob
  - family-names: Gabry
    given-names: Jonah
  - family-names: Kucukelbir
    given-names: Alp
  - family-names: Grant
    given-names: Robert
  - family-names: Tran
    given-names: Dustin
  - family-names: Malecki
    given-names: Michael
  - family-names: Gao
    given-names: Yuanjun
  - family-names: Badr
    given-names: Hamada S.
    email: badr@jhu.edu
    orcid: https://orcid.org/0000-0002-9808-2344
  year: '2025'
  doi: 10.32614/CRAN.package.StanHeaders
  version: '>= 2.26.0'

GitHub Events

Total

Create event: 261
Release event: 3
Issues event: 156
Watch event: 18
Delete event: 209
Issue comment event: 473
Push event: 642
Pull request review comment event: 348
Pull request review event: 513
Pull request event: 305
Fork event: 4

Last Year

Create event: 261
Release event: 3
Issues event: 156
Watch event: 18
Delete event: 209
Issue comment event: 473
Push event: 642
Pull request review comment event: 348
Pull request review event: 513
Pull request event: 305
Fork event: 4

Committers

Last synced: 8 months ago

All Time

Total Commits: 1,647
Total Committers: 29
Avg Commits per committer: 56.793
Development Distribution Score (DDS): 0.491

Past Year

Commits: 239
Committers: 12
Avg Commits per committer: 19.917
Development Distribution Score (DDS): 0.469

Top Committers

Name	Email	Commits
seabbs	s**2@g**m	839
Sebastian Funk	s**k@l**k	401
James Azam	j**m@l**k	157
Joe Hickson	j**n@m**k	56
seabbs	s**2@g**m	48
github-actions[bot]	4****]	41
seabbs	s**t@g**m	21
dependabot[bot]	4****]	18
Hamada S. Badr	h**r@g**m	16
Pietro Monticone	3****e	11
GitHub Action	a**n@g**m	7
Peter Ellis	p**z@g**m	5
github-merge-queue[bot]	1****]	4
Kaitlyn Johnson	9****n	3
jdmunday	1****y	3
JAllen42	j**2@g**m	2
Hugo Gruson	1****o	2
Carl A. B. Pearson	p****a	2
Adam Kucharski	a**i@l**k	1
Aki Vehtari	a**i@a**i	1
Sebastian Funk	s**b@m**n	1
Michael DeWitt	m**t@c**m	1
Joel Hellewell	j**4@i**k	1
Andrew Johnson	a**n@a**m	1
Lloyd Chapman	2****n	1
Michael DeWitt	m**r@g**m	1
Nikos Bosse	3****e	1
Sophie Meakin	s**n@o**m	1
Zachary Susswein	4****n	1

Committer Domains (Top 20 + Academic)

lshtm.ac.uk: 3 arjohnsonau.com: 1 imperial.ac.uk: 1 conehealth.com: 1 mac-c02dpd7tml7h.lan: 1 aalto.fi: 1 github.com: 1 gmail.comm: 1 metoffice.gov.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 316
Total pull requests: 588
Average time to close issues: 3 months
Average time to close pull requests: 16 days
Total issue authors: 36
Total pull request authors: 20
Average comments per issue: 2.36
Average comments per pull request: 1.74
Merged pull requests: 417
Bot issues: 0
Bot pull requests: 182

Past Year

Issues: 116
Pull requests: 332
Average time to close issues: 13 days
Average time to close pull requests: 4 days
Issue authors: 16
Pull request authors: 11
Average comments per issue: 1.83
Average comments per pull request: 1.35
Merged pull requests: 209
Bot issues: 0
Bot pull requests: 155

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Top Authors

Issue Authors

sbfnk (145)
jamesmbaazam (77)
seabbs (44)
avallecam (12)
zsusswein (3)
jonathonmellor (3)
LloydChapman (2)
joshwlambert (2)
SamuelBrand1 (2)
pearsonca (2)
kaitejohnson (2)
furqan915 (2)
damonbayer (2)
jcken95 (1)
dependabot[bot] (1)

Pull Request Authors

sbfnk (321)
github-actions[bot] (212)
jamesmbaazam (124)
seabbs (66)
dependabot[bot] (26)
kaitejohnson (11)
Bisaloo (4)
adamkucharski (3)
pearsonca (2)
jcken95 (2)
zsusswein (2)
avehtari (2)
LloydChapman (1)
medewitt (1)
smkerr (1)

Top Labels

Issue Labels

enhancement (24) bug (20) help wanted (12) question (11) documentation (8) good first issue (7) high priority (3) develop (2) refactor (2) discussion (1) low priority (1) wontfix (1) dependencies (1)

Pull Request Labels

documentation (207) dependencies (26) enhancement (5) bug (3) high priority (1) refactor (1) discussion (1) low priority (1) github_actions (1)

Dependencies

DESCRIPTION cran

R >= 3.4.0 depends
R.utils >= 2.0.0 imports
Rcpp >= 0.12.0 imports
RcppParallel >= 5.0.1 imports
cowplot * imports
data.table * imports
futile.logger >= 1.4 imports
future * imports
future.apply * imports
ggplot2 * imports
lifecycle * imports
lubridate * imports
methods * imports
patchwork * imports
progressr * imports
purrr * imports
rlang >= 0.4.7 imports
rstan >= 2.21.1 imports
rstantools >= 2.1.1 imports
runner * imports
scales * imports
stats * imports
truncnorm * imports
utils * imports
EpiSoon * suggests
countrycode * suggests
covr * suggests
dplyr * suggests
forecastHybrid * suggests
here * suggests
kableExtra * suggests
knitr * suggests
magrittr * suggests
precommit * suggests
rmarkdown * suggests
rnaturalearth * suggests
spelling * suggests
styler * suggests
testthat * suggests
tidyr * suggests

.github/workflows/R-CMD-as-cran-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/build-and-push-image.yaml actions

actions/checkout v2 composite
docker/build-push-action v2 composite
docker/login-action v1 composite
docker/metadata-action v2 composite
n1hility/cancel-previous-runs v2 composite

.github/workflows/lint-only-changed-files.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pr-commands.yaml actions

actions/checkout v2 composite
r-lib/actions/pr-fetch v1 composite
r-lib/actions/pr-push v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/render-readme.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/synthetic-validation.yaml actions

actions/checkout master composite
actions/upload-artifact v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/touchstone-comment.yaml actions

lorenzwalthert/touchstone/actions/comment v1 composite

.github/workflows/touchstone-receive.yaml actions

actions/checkout v2 composite
lorenzwalthert/touchstone/actions/receive v1 composite

.devcontainer/Dockerfile docker

rocker/r-ver ${VARIANT} build

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

epinow2

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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Top Labels

Issue Labels

Pull Request Labels

Dependencies