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primarycensored

Primary event censored distributions.

https://github.com/epinowcast/primarycensored

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.5%) to scientific vocabulary

Keywords

censoring distributions mc-stan r-package truncation
Last synced: 6 months ago · JSON representation ·

Repository

Primary event censored distributions.

Basic Info
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 6
  • Open Issues: 25
  • Releases: 9
Topics
censoring distributions mc-stan r-package truncation
Created over 1 year 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
)
```
# Primary event censored distributions primarycensored 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/primarycensored/workflows/R-CMD-check/badge.svg)](https://github.com/epinowcast/primarycensored/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epinowcast/primarycensored/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/primarycensored)

[![Universe](https://epinowcast.r-universe.dev/badges/primarycensored)](https://epinowcast.r-universe.dev/primarycensored)
[![MIT
license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/primarycensored/blob/master/LICENSE.md/)
[![](https://cranlogs.r-pkg.org/badges/grand-total/primarycensored)](https://CRAN.R-project.org/package=primarycensored)
[![GitHub contributors](https://img.shields.io/github/contributors/epinowcast/primarycensored)](https://github.com/epinowcast/primarycensored/graphs/contributors)
[![DOI](https://zenodo.org/badge/845633278.svg)](https://zenodo.org/doi/10.5281/zenodo.13632838)


## Summary

```{r, results = "asis", echo=FALSE}
cat(gsub("\n[ ]+", " ", packageDescription("primarycensored")$Description))
```

## Installation


Installing the package

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





Installing CmdStan (optional for Stan functionality)

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.*




## Resources

We provide a range of other documentation, case studies, and community spaces to ask (and answer!) questions:


Package Website

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/).





Vignettes

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.





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 you do not use `primarycensored`.




## 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 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, 
SamuelBrand1, 
sbfnk, 
athowes, 
jamesmbaazam, 
barbora-sobolova, 
pearsonca



### Issue Authors


zsusswein, 
jcblemai, 
adamkucharski



### Issue Contributors


parksw3

Owner

  • Name: Epinowcast
  • Login: epinowcast
  • Kind: organization

Flexible hierarchical nowcasting

Citation (CITATION.cff) 

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          "@type": "Person",
          "givenName": "Sam",
          "familyName": "Brand",
          "email": "usi1@cdc.gov",
          "@id": "https://orcid.org/0000-0003-0645-5367"
        },
        {
          "@type": "Person",
          "givenName": "James Mba",
          "familyName": "Azam",
          "email": "james.azam@lshtm.ac.uk",
          "@id": "https://orcid.org/0000-0001-5782-7330"
        },
        {
          "@type": "Person",
          "givenName": "Carl",
          "familyName": "Pearson",
          "email": "carl.ab.pearson@gmail.com",
          "@id": "https://orcid.org/0000-0003-0701-7860"
        },
        {
          "@type": "Person",
          "givenName": "Sebastian",
          "familyName": "Funk",
          "email": "sebastian.funk@lshtm.ac.uk",
          "@id": "https://orcid.org/0000-0002-2842-3406"
        },
        {
          "@type": "Person",
          "givenName": "Kelly",
          "familyName": "Charniga",
          "email": "kelly.charniga@gmail.com",
          "@id": "https://orcid.org/0000-0002-7648-7041"
        }
      ],
      "name": "primarycensored: Primary Event Censored Distributions",
      "identifier": "10.5281/zenodo.13632839",
      "@id": "https://doi.org/10.5281/zenodo.13632839",
      "sameAs": "https://doi.org/10.5281/zenodo.13632839"
    }
  ],
  "releaseNotes": "https://github.com/epinowcast/primarycensored/blob/master/NEWS.md",
  "readme": "https://github.com/epinowcast/primarycensored/blob/main/README.md",
  "contIntegration": [
    "https://github.com/epinowcast/primarycensored/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/epinowcast/primarycensored"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#stable",
  "keywords": [
    "censoring",
    "distributions",
    "truncation",
    "mc-stan",
    "r-package"
  ]
}

GitHub Events

Total
  • Create event: 57
  • Release event: 3
  • Issues event: 34
  • Watch event: 1
  • Delete event: 56
  • Member event: 1
  • Issue comment event: 100
  • Push event: 151
  • Pull request review comment event: 28
  • Pull request review event: 72
  • Pull request event: 121
  • Fork event: 4
Last Year
  • Create event: 57
  • Release event: 3
  • Issues event: 34
  • Watch event: 1
  • Delete event: 56
  • Member event: 1
  • Issue comment event: 100
  • Push event: 151
  • Pull request review comment event: 28
  • Pull request review event: 72
  • Pull request event: 121
  • Fork event: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 18
  • Total pull requests: 31
  • Average time to close issues: 4 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 4
  • Total pull request authors: 6
  • Average comments per issue: 0.72
  • Average comments per pull request: 0.84
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 21
Past Year
  • Issues: 18
  • Pull requests: 31
  • Average time to close issues: 4 months
  • Average time to close pull requests: 8 days
  • Issue authors: 4
  • Pull request authors: 6
  • Average comments per issue: 0.72
  • Average comments per pull request: 0.84
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 21
View more stats
Top Authors
Issue Authors
  • seabbs (11)
  • athowes (6)
  • sbfnk (2)
  • SamuelBrand1 (2)
  • github-actions[bot] (1)
  • adamkucharski (1)
  • jamesmbaazam (1)
Pull Request Authors
  • github-actions[bot] (50)
  • seabbs (8)
  • dependabot[bot] (6)
  • sbfnk (3)
  • jamesmbaazam (2)
  • barbora-sobolova (1)
  • athowes (1)
  • pearsonca (1)
Top Labels
Issue Labels
bug (3) documentation (3) enhancement (2) metadata (1) help wanted (1) good first issue (1)
Pull Request Labels
documentation (29) metadata (21) dependencies (6) github_actions (1) good first issue (1) blocked (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 250 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: primarycensored

Primary Event Censored Distributions

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 250 Last month
Rankings
Dependent packages count: 27.9%
Dependent repos count: 34.4%
Average: 49.7%
Downloads: 86.9%
Maintainers (1)
contact@samabbott.co.uk
Last synced: 7 months ago

Dependencies

.github/workflows/R-CMD-as-cran-check.yaml actions
  • actions/checkout v4 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 v4 composite
  • epinowcast/actions/install-cmdstan v1 composite
  • n1hility/cancel-previous-runs 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/check-cmdstan.yaml actions
  • actions/checkout v4 composite
  • epinowcast/actions/install-cmdstan v1 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/codemeta.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/lint-changed-files.yaml actions
  • actions/checkout v4 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 v4.6.3 composite
  • actions/checkout v4 composite
  • epinowcast/actions/install-cmdstan v1 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/render-readme.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • peter-evans/create-pull-request v6 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/render-stan-docs.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • mattnotmitt/doxygen-action v1.9.8 composite
  • peaceiris/actions-gh-pages v4 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
  • epinowcast/actions/install-cmdstan v1 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.0.0 depends
  • spelling >= 2.3.0 imports
  • knitrspelling * suggests
  • testthat >= 3.1.9 suggests
  • usethis * suggests
  • vdiffr * suggests
  • withr * suggests
.github/workflows/pr-commands.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite