epinowcast

Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

https://github.com/epinowcast/epinowcast

Science Score: 64.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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Links to: zenodo.org
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4 of 20 committers (20.0%) from academic institutions
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Institutional organization owner
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Scientific vocabulary similarity
Low similarity (21.9%) to scientific vocabulary

Keywords

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

Keywords from Contributors

covid-19 open-science r6 regional-data mesh parallel ode simulations distribution energy-system

Last synced: 6 months ago · JSON representation ·

Repository

Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

Basic Info

Host: GitHub
Owner: epinowcast
License: other
Language: R
Default Branch: main
Homepage: https://package.epinowcast.org/
Size: 365 MB

Statistics

Stars: 62
Watchers: 4
Forks: 22
Open Issues: 110
Releases: 9

Topics

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

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation Codeowners Codemeta

README.Rmd

---
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
)
```
# Flexible Hierarchical Nowcasting 


[![Lifecycle:
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
[![R-CMD-check](https://github.com/epinowcast/epinowcast/workflows/R-CMD-check/badge.svg)](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))
```

## 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) and to [highlight other features with 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

Owner

Name: Epinowcast
Login: epinowcast
Kind: organization

Website: epinowcast.org
Twitter: epinowcast
Repositories: 1
Profile: https://github.com/epinowcast

Flexible hierarchical nowcasting

Citation (CITATION.cff)

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# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "epinowcast" in publications use:'
type: software
license: MIT
title: 'epinowcast: Flexible Hierarchical Nowcasting'
version: 0.2.3.2000
doi: 10.5281/zenodo.5637165
abstract: 'Tools to enable flexible and efficient hierarchical nowcasting of right-truncated
  epidemiological time-series using a semi-mechanistic Bayesian model with support
  for a range of reporting and generative processes. Nowcasting, in this context,
  is gaining situational awareness using currently available observations and the
  reporting patterns of historical observations. This can be useful when tracking
  the spread of infectious disease in real-time: without nowcasting, changes in trends
  can be obfuscated by partial reporting or their detection may be delayed due to
  the use of simpler methods like truncation. While the package has been designed
  with epidemiological applications in mind, it could be applied to any set of right-truncated
  time-series count data.'
authors:
- name: Sam Abbott
  email: contact@samabbott.co.uk
  orcid: https://orcid.org/0000-0001-8057-8037
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  given-names: Adrian
  email: adrian.lison@bsse.ethz.ch
  orcid: https://orcid.org/0000-0002-6822-8437
- family-names: Funk
  given-names: Sebastian
  email: sebastian.funk@lshtm.ac.uk
- family-names: Pearson
  given-names: Carl
  email: carl.ab.pearson@gmail.com
  orcid: https://orcid.org/0000-0003-0701-7860
- family-names: Gruson
  given-names: Hugo
  email: hugo.gruson@normalesup.org
  orcid: https://orcid.org/0000-0002-4094-1476
- family-names: Guenther
  given-names: Felix
  email: felixguenther1@gmx.de
  orcid: https://orcid.org/0000-0001-6582-1174
preferred-citation:
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  doi: 10.5281/zenodo.5637165
repository-code: https://github.com/epinowcast/epinowcast/issues/
url: https://package.epinowcast.org
contact:
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  notes: Imports
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  notes: Imports
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    email: guojq28@gmail.com
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    given-names: Nikos
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CodeMeta (codemeta.json)

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      "@type": "Organization",
      "name": "Sam Abbott",
      "email": "sam.abbott@lshtm.ac.uk",
      "@id": "https://orcid.org/0000-0001-8057-8037"
    },
    {
      "@type": "Person",
      "givenName": "Adrian",
      "familyName": "Lison",
      "email": "adrian.lison@bsse.ethz.ch",
      "@id": "https://orcid.org/0000-0002-6822-8437"
    }
  ],
  "contributor": [
    {
      "@type": "Person",
      "givenName": "Michael",
      "familyName": "DeWitt",
      "email": "me.dewitt.jr@gmail.com",
      "@id": "https://orcid.org/0000-0001-8940-1967"
    }
  ],
  "maintainer": [
    {
      "@type": "Organization",
      "name": "Sam Abbott",
      "email": "sam.abbott@lshtm.ac.uk",
      "@id": "https://orcid.org/0000-0001-8057-8037"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "loo",
      "name": "loo",
      "version": ">= 2.4.1",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://github.com/stan-dev/loo"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "scoringutils",
      "name": "scoringutils",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=scoringutils"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=spelling"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "usethis",
      "name": "usethis",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=usethis"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "vdiffr",
      "name": "vdiffr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=vdiffr"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.5.0"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "cmdstanr",
      "name": "cmdstanr",
      "sameAs": "https://github.com/stan-dev/cmdstanr"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "data.table",
      "name": "data.table",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=data.table"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "lubridate",
      "name": "lubridate",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=lubridate"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "lme4",
      "name": "lme4",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=lme4"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "ggplot2",
      "name": "ggplot2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "posterior",
      "name": "posterior",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=posterior"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "purrr",
      "name": "purrr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=purrr"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "rstan",
      "name": "rstan",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rstan"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "scales",
      "name": "scales",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=scales"
    },
    "SystemRequirements": "CmdStan (>=2.29)"
  },
  "fileSize": "100828.43KB",
  "citation": [
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2021",
      "author": [
        {
          "@type": "Person",
          "givenName": "Sam",
          "familyName": "Abbott"
        }
      ],
      "name": "epinowcast: Hierarchical nowcasting of right censored epidemiological counts",
      "identifier": "10.5281/zenodo.5637165",
      "@id": "https://doi.org/10.5281/zenodo.5637165",
      "sameAs": "https://doi.org/10.5281/zenodo.5637165",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2021",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "name": "Zenodo"
        }
      }
    }
  ],
  "releaseNotes": "https://github.com/epinowcast/epinowcast/blob/master/NEWS.md",
  "readme": "https://github.com/epinowcast/epinowcast/blob/main/README.md",
  "contIntegration": [
    "https://github.com/epinowcast/epinowcast/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/epinowcast/epinowcast"
  ],
  "developmentStatus": "https://www.tidyverse.org/lifecycle/#experimental",
  "keywords": [
    "nowcasting",
    "stan",
    "cmdstanr",
    "epidemiology"
  ]
}

GitHub Events

Total

Issues event: 14
Watch event: 5
Delete event: 26
Issue comment event: 32
Push event: 51
Pull request review event: 20
Pull request event: 77
Fork event: 1
Create event: 42

Last Year

Issues event: 14
Watch event: 5
Delete event: 26
Issue comment event: 32
Push event: 51
Pull request review event: 20
Pull request event: 77
Fork event: 1
Create event: 42

Committers

Last synced: about 2 years ago

All Time

Total Commits: 753
Total Committers: 20
Avg Commits per committer: 37.65
Development Distribution Score (DDS): 0.478

Past Year

Commits: 133
Committers: 14
Avg Commits per committer: 9.5
Development Distribution Score (DDS): 0.338

Top Committers

Name	Email	Commits
Sam Abbott	c**t@s**k	393
Sam Abbott	s**2@g**m	190
Adrian Lison	a**n@b**h	73
Adrian Lison	a**n@e**h	26
Sebastian Funk	s**k@l**k	12
Hugo Gruson	B****o	10
dependabot[bot]	4****]	9
Carl A. B. Pearson	p****a	7
Michael DeWitt	c**a@c**m	6
choi-hannah	6****h	6
Michael DeWitt	m**r@g**m	4
seabbs	s****s	4
Pietro Monticone	3****e	4
James Azam	j**m@l**k	2
Kath Sherratt	6****t	2
James Azam	j**m@g**m	1
Nate McIntosh	N**h@c**v	1
Nikos Bosse	3****e	1
Luis Rivas	6****s	1
Pratik Gupte	p**6@g**m	1

Committer Domains (Top 20 + Academic)

lshtm.ac.uk: 2 cdc.gov: 1 conehealth.com: 1 ethz.ch: 1 bsse.ethz.ch: 1 samabbott.co.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 135
Total pull requests: 120
Average time to close issues: 3 months
Average time to close pull requests: 12 days
Total issue authors: 17
Total pull request authors: 15
Average comments per issue: 2.27
Average comments per pull request: 4.95
Merged pull requests: 76
Bot issues: 0
Bot pull requests: 42

Past Year

Issues: 9
Pull requests: 36
Average time to close issues: 10 days
Average time to close pull requests: 10 days
Issue authors: 7
Pull request authors: 4
Average comments per issue: 0.0
Average comments per pull request: 0.25
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 33

View more stats

Top Authors

Issue Authors

seabbs (93)
pearsonca (10)
adrian-lison (9)
jamesmbaazam (6)
natemcintosh (5)
jessalynnsebastian (3)
Bisaloo (3)
medewitt (3)
zsusswein (3)
sbfnk (3)
athowes (2)
jbracher (2)
teojcryan (1)
github-actions[bot] (1)
beansrowning (1)

Pull Request Authors

seabbs (60)
github-actions[bot] (50)
dependabot[bot] (23)
Bisaloo (9)
adrian-lison (8)
medewitt (7)
pearsonca (6)
sbfnk (5)
jamesmbaazam (5)
athowes (4)
jessalynnsebastian (3)
jimrothstein (2)
kathsherratt (2)
nikosbosse (2)
Lnrivas (1)

Top Labels

Issue Labels

enhancement (72) help wanted (56) documentation (29) bug (21) good first issue (17) high-priority (15) infrastructure (14) low-priority (9) question (9) stan (3) dependencies (1) wontfix (1) todo :spiral_notepad: (1)

Pull Request Labels

documentation (59) dependencies (23) enhancement (10) infrastructure (4) high-priority (4) bug (3) help wanted (3) self-reviewed (2) todo :spiral_notepad: (1) good first issue (1) wontfix (1) stuck (1) github_actions (1)

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
cmdstanr * imports
data.table * imports
ggplot2 * imports
lubridate * imports
posterior * imports
purrr * imports
rstan * imports
scales * imports
knitr * suggests
loo >= 2.4.1 suggests
rmarkdown * suggests
scoringutils * suggests
spelling * suggests
testthat >= 3.0.0 suggests
usethis * suggests
vdiffr * 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 v2 composite
n1hility/cancel-previous-runs 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/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/codemeta.yaml actions

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

.github/workflows/lint.yaml actions

actions/checkout v2 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 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

.devcontainer/Dockerfile docker

rocker/r-ver ${VARIANT} build

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

epinowcast

Science Score: 64.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

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

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies