Data

Tools

Indexes

Applications

Experiments

Open Source Science

baylum

Chronological Bayesian models integrated for Optically Stimulated Luminescence (OSL) Dating

https://github.com/crp2a/baylum

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 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 (19.8%) to scientific vocabulary

Keywords

archaeometry bayesian-statistics geochronology luminescence-dating r-package radiocarbon-dates
Last synced: 4 months ago · JSON representation

Repository

Chronological Bayesian models integrated for Optically Stimulated Luminescence (OSL) Dating

Basic Info
Statistics
  • Stars: 9
  • Watchers: 7
  • Forks: 2
  • Open Issues: 0
  • Releases: 9
Topics
archaeometry bayesian-statistics geochronology luminescence-dating r-package radiocarbon-dates
Created over 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Codemeta Zenodo

README.Rmd 

---
output: github_document
header-includes:
   - \usepackage{amsmath}
   - \usepackage{amssymb}
---


```{r, echo = FALSE, message=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
library(BayLum)
```
 
# BayLum 


[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)

[![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
[![CRAN Version](https://www.r-pkg.org/badges/version/BayLum)](https://cran.r-project.org/package=BayLum)
[![CRAN checks](https://badges.cranchecks.info/worst/BayLum.svg)](https://cran.r-project.org/web/checks/check_results_BayLum.html)
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/BayLum)](https://cran.r-project.org/package=BayLum)

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![DOI Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.4311266.svg)](https://doi.org/10.5281/zenodo.4311266)
[![CRAN DOI](https://img.shields.io/badge/doi-10.32614/CRAN.package.BayLum-blue.svg)](https://doi.org/10.32614/CRAN.package.BayLum)


An R package for chronological **Bay**esian models integrated for Optically Stimulated (OSL) **Lum**inescence Dating

```{r citation, echo=FALSE, comment=''}
cite <- utils::citation("BayLum")
print(cite, bibtex = FALSE)
```

## Installation

**You need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on your computer.**

You can install the released version of **BayLum** from [CRAN](https://CRAN.R-project.org) with:

```{r cran-installation, eval=FALSE}
install.packages("BayLum")
```

And the development version from [GitHub](https://github.com/) with:

```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_github("crp2a/BayLum")
```

Please note that development versions may change day by day.

## License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

## Acknowledgements

The development of **BayLum** received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. ANR-10-LABX-52) between 2015 and 2018.

Owner

  • Name: Archéosciences Bordeaux
  • Login: crp2a
  • Kind: organization
  • Location: Pessac, France

Archaeological Science Laboratory at Bordeaux Montaigne University

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "BayLum",
  "description": "Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.",
  "name": "BayLum: Chronological Bayesian Models Integrating Optically Stimulated\n    Luminescence and Radiocarbon Age Dating",
  "relatedLink": [
    "https://CRAN.r-project.org/package=BayLum",
    "https://CRAN.R-project.org/package=BayLum"
  ],
  "codeRepository": "https://github.com/crp2a/BayLum",
  "issueTracker": "https://github.com/crp2a/BayLum/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.3.3",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R Under development (unstable) (2025-09-18 r88857)",
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "author": [
    {
      "@type": "Person",
      "givenName": "Claire",
      "familyName": "Christophe"
    },
    {
      "@type": "Person",
      "givenName": "Anne",
      "familyName": "Philippe",
      "email": "anne.philippe@univ-nantes.fr",
      "@id": "https://orcid.org/0000-0002-5331-5087"
    },
    {
      "@type": "Person",
      "givenName": "Sebastian",
      "familyName": "Kreutzer",
      "@id": "https://orcid.org/0000-0002-0734-2199"
    },
    {
      "@type": "Person",
      "givenName": "Guillaume",
      "familyName": "Guérin",
      "@id": "https://orcid.org/0000-0001-6298-5579"
    },
    {
      "@type": "Person",
      "givenName": "Frederik Harly",
      "familyName": "Baumgarten",
      "@id": "https://orcid.org/0000-0002-4374-5948"
    },
    {
      "@type": "Person",
      "givenName": "Nicolas",
      "familyName": "Frerebeau",
      "@id": "https://orcid.org/0000-0001-5759-4944"
    }
  ],
  "copyrightHolder": [
    {
      "@type": "Organization",
      "name": "Université Bordeaux Montaigne"
    }
  ],
  "funder": [
    {
      "@type": "Organization",
      "name": "Université Bordeaux Montaigne"
    },
    {
      "@type": "Organization",
      "name": "CNRS"
    },
    {
      "@type": "Organization",
      "name": "LabEx Sciences archéologiques de Bordeaux"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Anne",
      "familyName": "Philippe",
      "email": "anne.philippe@univ-nantes.fr",
      "@id": "https://orcid.org/0000-0002-5331-5087"
    }
  ],
  "softwareSuggestions": [
    {
      "@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": "testthat",
      "name": "testthat",
      "version": ">= 3.2.3",
      "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"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "coda",
      "name": "coda",
      "version": ">= 0.19",
      "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=coda"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 4.4"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "utils",
      "name": "utils"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "cli",
      "name": "cli",
      "version": ">= 3.6.5",
      "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=cli"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "hexbin",
      "name": "hexbin",
      "version": ">= 1.28.5",
      "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=hexbin"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "KernSmooth",
      "name": "KernSmooth",
      "version": ">= 2.23",
      "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=KernSmooth"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "Luminescence",
      "name": "Luminescence",
      "version": ">= 1.1.1",
      "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=Luminescence"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "methods",
      "name": "methods"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "rjags",
      "name": "rjags",
      "version": ">= 4-17",
      "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=rjags"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "runjags",
      "name": "runjags",
      "version": ">= 2.2.2",
      "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=runjags"
    },
    "11": {
      "@type": "SoftwareApplication",
      "identifier": "yaml",
      "name": "yaml",
      "version": ">= 2.3.10",
      "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=yaml"
    },
    "SystemRequirements": "JAGS >= 4.3.2 (https://mcmc-jags.sourceforge.io/)"
  },
  "fileSize": "3365.616KB",
  "citation": [
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2025",
      "author": [
        {
          "@type": "Person",
          "givenName": "Claire",
          "familyName": "Christophe"
        },
        {
          "@type": "Person",
          "givenName": "Anne",
          "familyName": "Philippe",
          "email": "anne.philippe@univ-nantes.fr",
          "@id": "https://orcid.org/0000-0002-5331-5087"
        },
        {
          "@type": "Person",
          "givenName": "Sebastian",
          "familyName": "Kreutzer",
          "@id": "https://orcid.org/0000-0002-0734-2199"
        },
        {
          "@type": "Person",
          "givenName": "Guillaume",
          "familyName": "Guérin",
          "@id": "https://orcid.org/0000-0001-6298-5579"
        },
        {
          "@type": "Person",
          "givenName": "Frederik Harly",
          "familyName": "Baumgarten",
          "@id": "https://orcid.org/0000-0002-4374-5948"
        },
        {
          "@type": "Person",
          "givenName": "Nicolas",
          "familyName": "Frerebeau",
          "@id": "https://orcid.org/0000-0001-5759-4944"
        }
      ],
      "name": "BayLum: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating",
      "url": "https://CRAN.r-project.org/package=BayLum",
      "description": "R package version 0.3.3"
    },
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2019",
      "author": [
        {
          "@type": "Person",
          "givenName": "Anne",
          "familyName": "Philippe"
        },
        {
          "@type": "Person",
          "givenName": "Guillaume",
          "familyName": "Guerin"
        },
        {
          "@type": "Person",
          "givenName": "Sebastian",
          "familyName": "Kreutzer"
        }
      ],
      "name": "BayLum - An R package for Bayesian analysis of OSL ages: An introduction",
      "identifier": "10.1016/j.quageo.2018.05.009",
      "pagination": "16-24",
      "@id": "https://doi.org/10.1016/j.quageo.2018.05.009",
      "sameAs": "https://doi.org/10.1016/j.quageo.2018.05.009",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2019",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "49",
          "name": "Quaternary Geochronology"
        }
      }
    }
  ],
  "releaseNotes": "https://github.com/crp2a/BayLum/blob/main/NEWS.md",
  "readme": "https://github.com/crp2a/BayLum/blob/master/README.md",
  "contIntegration": [
    "https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/crp2a/BayLum"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "keywords": [
    "luminescence-dating",
    "bayesian-statistics",
    "radiocarbon-dates",
    "geochronology",
    "r-package",
    "archaeometry"
  ]
}

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • coda >= 0.19 depends
  • utils * depends
  • ArchaeoPhases >= 1.5 imports
  • KernSmooth >= 2.23 imports
  • Luminescence >= 0.9.18 imports
  • hexbin >= 1.28.2 imports
  • methods * imports
  • rjags >= 4 imports
  • runjags >= 2.2.0 imports
  • R.rsp >= 0.44.0 suggests
  • testthat >= 3.1.2 suggests
.github/workflows/GitHub_Actions_CI.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