baselinenowcast

In-development R package to nowcast right-truncated epidemiological data

https://github.com/epinowcast/baselinenowcast

Science Score: 44.0%

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
  • Academic publication links
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (18.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

In-development R package to nowcast right-truncated epidemiological data

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 2
  • Open Issues: 39
  • Releases: 2
Created about 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation 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
)
```
# Baseline nowcast baselinenowcast website



[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-yellow.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![R-CMD-check](https://github.com/epinowcast/baselinenowcast/workflows/R-CMD-check/badge.svg)](https://github.com/epinowcast/baselinenowcast/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epinowcast/baselinenowcast/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/baselinenowcast)
[![MIT
license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/baselinenowcast/blob/master/LICENSE.md/)
[![GitHub contributors](https://img.shields.io/github/contributors/epinowcast/baselinenowcast)](https://github.com/epinowcast/baselinenowcast/graphs/contributors)





## Summary

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

## Installation

Installing the package ```{r, child="vignettes/chunks/_readme-install-baselinenowcast.Rmd"} ```
## Resources We provide a range of other documentation, case studies, and community spaces to ask (and answer!) questions:
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 `baselinenowcast`.
## Contributing We welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/baselinenowcast/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/baselinenowcast/pulls) and see our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information. ### 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/baselinenowcast/issues). See our [contributing guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md) for more information. ### Code of Conduct Please note that the `baselinenowcast` 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 you use `baselinenowcast` in your work, please consider citing it with `citation("baselinenowcast")`. ## 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 kaitejohnson, seabbs, TimTaylor, sbfnk ### Issue Authors jonathonmellor, swo ### Issue Contributors jamesmbaazam, jbracher

Owner

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

Flexible hierarchical nowcasting

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------

cff-version: 1.2.0
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type: software
license: MIT
title: 'baselinenowcast: Baseline nowcast from right-truncated epidemiological data'
version: 0.1.0.1000
logo: "man/figures/logo.png"
keywords:
  - epidemiology
  - nowcasting
  - public-health
  - surveillance
  - forecasting
  - r-package
doi: 10.5281/zenodo.13632839
identifiers:
- type: url
  value: https://github.com/epinowcast/baselinenowcast/
abstract: This package provides R functions to implement nowcasting from
  right-truncated epidemiological case data
authors:
- name: Kaitlyn Johnson
  email: kaitlyn.johnson@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-8011-0012
- name: Sam Abbott
  email: contact@samabbott.co.uk
  orcid: https://orcid.org/0000-0001-8057-8037
- name: Sebastian Funk
  email: sebastian.funk@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-2842-3406
- name: Johannes Bracher
  email: johannes.bracher@kit.edu
  orcid: https://orcid.org/0000-0002-3777-1410
preferred-citation:
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  title: 'baselinenowcast: Baseline nowcast from right-truncated epidemiological data'
  authors:
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    email: kaitlyn.johnson@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8011-0012
  - name: Sam Abbott
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    orcid: https://orcid.org/0000-0001-8057-8037
  - name: Sebastian Funk
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    orcid: https://orcid.org/0000-0002-2842-3406
  - name: Johannes Bracher
    email: johannes.bracher@kit.edu
    orcid: https://orcid.org/0000-0002-3777-1410
  year: '2025'
repository-code: https://github.com/epinowcast/baselinenowcast/issues/
url: https://baselinenowcast.epinowcast.org
contact:
- name: Kaitlyn Johnson
  email: kaitlyn.johnson@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-8011-0012
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      "sameAs": "https://doi.org/10.1101/2025.08.14.25333653",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2025",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "name": "medRxiv"
        }
      }
    },
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2025",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Kaitlyn",
            "E."
          ],
          "familyName": "Johnson"
        },
        {
          "@type": "Person",
          "givenName": "Emily",
          "familyName": "Tyszka"
        },
        {
          "@type": "Person",
          "givenName": "Johannes",
          "familyName": "Bracher"
        },
        {
          "@type": "Person",
          "givenName": "Sebastian",
          "familyName": "Funk"
        },
        {
          "@type": "Person",
          "givenName": "Sam",
          "familyName": "Abbott"
        }
      ],
      "name": "baselinenowcast: Methods for baseline nowcasting right-truncated epidemiological data",
      "url": "https://github.com/epinowcast/baselinenowcast/"
    }
  ],
  "releaseNotes": "https://github.com/epinowcast/baselinenowcast/blob/main/NEWS.md",
  "readme": "https://github.com/epinowcast/baselinenowcast/blob/main/README.md",
  "contIntegration": [
    "https://github.com/epinowcast/baselinenowcast/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/epinowcast/baselinenowcast"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
}

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