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kairos

Analysis of Chronological Patterns from Archaeological Count Data - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/kairos

https://github.com/tesselle/kairos

Science Score: 77.0%

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 17 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.4%) to scientific vocabulary

Keywords

archaeological-science archaeology chronology matrix-seriation r-package
Last synced: 6 months ago · JSON representation ·

Repository

Analysis of Chronological Patterns from Archaeological Count Data - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/kairos

Basic Info
Statistics
  • Stars: 17
  • Watchers: 1
  • Forks: 1
  • Open Issues: 5
  • Releases: 10
Topics
archaeological-science archaeology chronology matrix-seriation r-package
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation Codemeta

README.Rmd 

---
output: github_document
bibliography: vignettes/bibliography.bib
nocite: '@*'
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = NULL
)
Sys.setenv(LANGUAGE = "en") # Force locale
```

# kairos 


[![status-badge](https://ci.codeberg.org/api/badges/14692/status.svg)](https://ci.codeberg.org/repos/14692){.pkgdown-devel}
[![Code coverage](https://packages.tesselle.org/kairos/coverage/badge.svg)](https://packages.tesselle.org/kairos/coverage/){.pkgdown-devel}
[![Dependencies](https://tinyverse.netlify.app/badge/kairos)](https://cran.r-project.org/package=kairos){.pkgdown-devel}

[![r-universe](https://tesselle.r-universe.dev/badges/kairos)](https://tesselle.r-universe.dev/kairos){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/kairos)](https://cran.r-project.org/package=kairos){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/kairos.svg)](https://cran.r-project.org/web/checks/check_results_kairos.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/kairos)](https://cran.r-project.org/package=kairos){.pkgdown-release}

[![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](https://zenodo.org/badge/DOI/10.5281/zenodo.5653896.svg)](https://doi.org/10.5281/zenodo.5653896)


## Overview

A toolkit for relative and absolute dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site. **kairos** provides methods for:

* Matrix seriation: `seriate_rank()` and `seriate_average()`.
* Testing matrix seriation results [@porcic2013; @peeples2012]: `assess()` and `refine()`.
* Mean ceramic date estimation [@south1977]: `mcd()`.
* Event and accumulation date estimation [@bellanger2012]: `event()`.
* Aoristic analysis [@ratcliffe2000]: `aoristic()`.
* Chronological apportioning [@roberts2012]: `apportion()`.

[**tabula**](https://packages.tesselle.org/tabula/) is a companion package to **kairos** that provides functions for visualization and analysis of archaeological count data.

---

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

## Installation

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

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

And the development version from [Codeberg](https://codeberg.org/) with:

```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_git("https://codeberg.org/tesselle/kairos")
```

## Usage

```{r packages-load}
## Load packages
library(kairos)
```

**kairos** uses [**aion**](https://packages.tesselle.org/aion/) for internal date representation. Look at `vignette("aion", package = "aion")` before you start.

*It assumes that you keep your data tidy*: each variable (type/taxa) must be saved in its own column and each observation (sample/case) must be saved in its own row.

```{r aoristic, fig.width=7, fig.height=6}
## Data from Husi 2022
data("loire", package = "folio")
keep <- c("Anjou", "Blésois", "Orléanais", "Haut-Poitou", "Touraine")
loire <- subset(loire, area %in% keep)

## Get time range
loire_range <- loire[, c("lower", "upper")]

## Calculate aoristic sum (weights) by group
ao <- aoristic(loire_range, step = 50, weight = TRUE, groups = loire$area)

## Plot
plot(ao, col = "grey")

## Rate of change by group
set.seed(12345) # Set seed for reproductibility
ro <- roc(ao, n = 30)
plot(ro)
```

## Translation

This package provides translations of user-facing communications, like messages, warnings and errors, and graphical elements (axis labels). The preferred language is by default taken from the locale. This can be overridden by setting of the environment variable `LANGUAGE` (you only need to do this once per session):

``` r
Sys.setenv(LANGUAGE = "")
```

Languages currently available are English (`en`) and French (`fr`).

## Contributing

Please note that the **kairos** project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project, you agree to abide by its terms.

## References

```{r metadata, include=FALSE}
## Update codemeta.json
codemetar::write_codemeta(verbose = FALSE)

## Update CITATION.cff
cff_keys <- list(
  identifiers = list(
    list(description = "The concept DOI.",
         type = "doi",
         value = "10.5281/zenodo.5653896"),
    list(description = "The versioned DOI for version 1.0.0.",
         type = "doi",
         value = "10.5281/zenodo.5653897"),
    list(description = "The versioned DOI for version 1.0.1.",
         type = "doi",
         value = "10.5281/zenodo.6349207"),
    list(description = "The versioned DOI for version 1.1.0.",
         type = "doi",
         value = "10.5281/zenodo.6659732"),
    list(description = "The versioned DOI for version 1.2.0.",
         type = "doi",
         value = "10.5281/zenodo.7307327"),
    list(description = "The versioned DOI for version 2.0.0.",
         type = "doi",
         value = "10.5281/zenodo.8301347"),
    list(description = "The versioned DOI for version 2.0.1.",
         type = "doi",
         value = "10.5281/zenodo.8318621"),
    list(description = "The versioned DOI for version 2.0.2.",
         type = "doi",
         value = "10.5281/zenodo.10209640"),
    list(description = "The versioned DOI for version 2.1.0.",
         type = "doi",
         value = "10.5281/zenodo.10711260"),
    list(description = "The versioned DOI for version 2.1.1.",
         type = "doi",
         value = "10.5281/zenodo.12967467"),
    list(description = "The versioned DOI for version 2.2.0.",
         type = "doi",
         value = "10.5281/zenodo.14357977"),
    list(description = "The versioned DOI for version 2.2.1.",
         type = "doi",
         value = "10.5281/zenodo.15132107"),
    list(description = "The versioned DOI for version 2.3.0.",
         type = "doi",
         value = "10.5281/zenodo.15463239"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.kairos")
  )
)
cff <- cffr::cff_create("DESCRIPTION", keys = cff_keys)
if (cffr::cff_validate(cff)) cffr::cff_write(cff, outfile = "CITATION.cff")
```

Owner

  • Name: tesselle
  • Login: tesselle
  • Kind: organization
  • Location: France

A collection of R packages for archaeological research and teaching

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 "kairos" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'kairos: Analysis of Chronological Patterns from Archaeological Count Data'
version: 2.3.0
doi: 10.5281/zenodo.5653896
identifiers:
- description: The concept DOI.
  type: doi
  value: 10.5281/zenodo.5653896
- description: The versioned DOI for version 1.0.0.
  type: doi
  value: 10.5281/zenodo.5653897
- description: The versioned DOI for version 1.0.1.
  type: doi
  value: 10.5281/zenodo.6349207
- description: The versioned DOI for version 1.1.0.
  type: doi
  value: 10.5281/zenodo.6659732
- description: The versioned DOI for version 1.2.0.
  type: doi
  value: 10.5281/zenodo.7307327
- description: The versioned DOI for version 2.0.0.
  type: doi
  value: 10.5281/zenodo.8301347
- description: The versioned DOI for version 2.0.1.
  type: doi
  value: 10.5281/zenodo.8318621
- description: The versioned DOI for version 2.0.2.
  type: doi
  value: 10.5281/zenodo.10209640
- description: The versioned DOI for version 2.1.0.
  type: doi
  value: 10.5281/zenodo.10711260
- description: The versioned DOI for version 2.1.1.
  type: doi
  value: 10.5281/zenodo.12967467
- description: The versioned DOI for version 2.2.0.
  type: doi
  value: 10.5281/zenodo.14357977
- description: The versioned DOI for version 2.2.1.
  type: doi
  value: 10.5281/zenodo.15132107
- description: The versioned DOI for version 2.3.0.
  type: doi
  value: 10.5281/zenodo.15463239
- description: The CRAN DOI
  type: doi
  value: 10.32614/cran.package.kairos
abstract: A toolkit for absolute and relative dating and analysis of chronological
  patterns. This package includes functions for chronological modeling and dating
  of archaeological assemblages from count data. It provides methods for matrix seriation.
  It also allows to compute time point estimates and density estimates of the occupation
  and duration of an archaeological site.
authors:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
preferred-citation:
  type: manual
  title: 'kairos: Analysis of Chronological Patterns from Archaeological Count Data'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  institution:
    name: Université Bordeaux Montaigne
    address: Pessac, France
  notes: R package version 2.3.0
  url: https://packages.tesselle.org/kairos/
  doi: 10.5281/zenodo.5653896
repository: https://CRAN.R-project.org/package=kairos
repository-code: https://codeberg.org/tesselle/kairos
url: https://packages.tesselle.org/kairos/
contact:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
keywords:
- chronology
- matrix-seriation
- archaeology
- archaeological-science
- r-package
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 3.5'
- type: software
  title: aion
  abstract: 'aion: Archaeological Time Series'
  notes: Depends
  url: https://packages.tesselle.org/aion/
  repository: https://CRAN.R-project.org/package=aion
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  - family-names: Roe
    given-names: Joe
    email: joseph.roe@iaw.unibe.ch
    orcid: https://orcid.org/0000-0002-1011-1244
  doi: 10.32614/CRAN.package.aion
  version: '>= 1.5.0'
  year: '2025'
- type: software
  title: dimensio
  abstract: 'dimensio: Multivariate Data Analysis'
  notes: Depends
  url: https://packages.tesselle.org/dimensio/
  repository: https://CRAN.R-project.org/package=dimensio
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  doi: 10.32614/CRAN.package.dimensio
  version: '>= 0.13.0'
  year: '2025'
- type: software
  title: arkhe
  abstract: 'arkhe: Tools for Cleaning Rectangular Data'
  notes: Imports
  url: https://packages.tesselle.org/arkhe/
  repository: https://CRAN.R-project.org/package=arkhe
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  doi: 10.32614/CRAN.package.arkhe
  version: '>= 1.11.0'
- type: software
  title: extraDistr
  abstract: 'extraDistr: Additional Univariate and Multivariate Distributions'
  notes: Imports
  url: https://github.com/twolodzko/extraDistr
  repository: https://CRAN.R-project.org/package=extraDistr
  authors:
  - family-names: Wolodzko
    given-names: Tymoteusz
  year: '2025'
  doi: 10.32614/CRAN.package.extraDistr
- type: software
  title: grDevices
  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: methods
  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: 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: 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: folio
  abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
  notes: Suggests
  url: https://packages.tesselle.org/folio/
  repository: https://CRAN.R-project.org/package=folio
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  doi: 10.32614/CRAN.package.folio
  version: '>= 1.5.0'
  year: '2025'
- type: software
  title: fontquiver
  abstract: 'fontquiver: Set of Installed Fonts'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=fontquiver
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.fontquiver
- 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: markdown
  abstract: 'markdown: Render Markdown with ''commonmark'''
  notes: Suggests
  url: https://github.com/rstudio/markdown
  repository: https://CRAN.R-project.org/package=markdown
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Allaire
    given-names: JJ
  - family-names: Horner
    given-names: Jeffrey
  year: '2025'
  doi: 10.32614/CRAN.package.markdown
- type: software
  title: rsvg
  abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
    Bitmap Arrays'
  notes: Suggests
  url: https://docs.ropensci.org/rsvg/
  repository: https://CRAN.R-project.org/package=rsvg
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2025'
  doi: 10.32614/CRAN.package.rsvg
- type: software
  title: svglite
  abstract: 'svglite: An ''SVG'' Graphics Device'
  notes: Suggests
  url: https://svglite.r-lib.org
  repository: https://CRAN.R-project.org/package=svglite
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2025'
  doi: 10.32614/CRAN.package.svglite
- type: software
  title: tabula
  abstract: 'tabula: Analysis and Visualization of Archaeological Count Data'
  notes: Suggests
  url: https://packages.tesselle.org/tabula/
  repository: https://CRAN.R-project.org/package=tabula
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  doi: 10.32614/CRAN.package.tabula
  version: '>= 3.3.0'
  year: '2025'
- type: software
  title: tinysnapshot
  abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
  notes: Suggests
  url: https://github.com/vincentarelbundock/tinysnapshot
  repository: https://CRAN.R-project.org/package=tinysnapshot
  authors:
  - family-names: Arel-Bundock
    given-names: Vincent
    email: vincent.arel-bundock@umontreal.ca
    orcid: https://orcid.org/0000-0003-2042-7063
  year: '2025'
  doi: 10.32614/CRAN.package.tinysnapshot
- type: software
  title: tinytest
  abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework'
  notes: Suggests
  url: https://github.com/markvanderloo/tinytest
  repository: https://CRAN.R-project.org/package=tinytest
  authors:
  - family-names: Loo
    given-names: Mark
    name-particle: van der
    email: mark.vanderloo@gmail.com
    orcid: https://orcid.org/0000-0002-9807-4686
  year: '2025'
  doi: 10.32614/CRAN.package.tinytest

CodeMeta (codemeta.json) 

{
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  "description": "A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.",
  "name": "kairos: Analysis of Chronological Patterns from Archaeological Count Data",
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}

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Watch event: 2
  • Push event: 22
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Watch event: 2
  • Push event: 22

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 104
  • Total Committers: 1
  • Avg Commits per committer: 104.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 33
  • Committers: 1
  • Avg Commits per committer: 33.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
nfrerebeau n****u@u****r 104
Committer Domains (Top 20 + Academic)
u-bordeaux-montaigne.fr: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 10
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.3
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nfrerebeau (8)
  • topographos (2)
Pull Request Authors
Top Labels
Issue Labels
feature (6) documentation (1) enhancement (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • Hmisc * imports
  • arkhe >= 1.0.0 imports
  • dimensio >= 0.3.0 imports
  • extraDistr * imports
  • ggplot2 * imports
  • grDevices * imports
  • methods * imports
  • rlang * imports
  • stats * imports
  • utils * imports
  • covr * suggests
  • folio >= 1.3.0 suggests
  • khroma * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • tabula >= 2.0.0 suggests
  • testthat >= 3.0.0 suggests
  • vdiffr >= 1.0.0 suggests