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aion

aion: An R Package to Represent Archaeological Time Series - Published in JOSS (2024)

https://github.com/tesselle/aion

Science Score: 100.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
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    Found codemeta.json file
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    Found .zenodo.json file
  • ✓
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    Found 19 DOI reference(s) in README and JOSS metadata
  • ✓
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    Links to: joss.theoj.org, zenodo.org
  • ✓
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    1 of 1 committers (100.0%) from academic institutions
  • ○
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    Published in Journal of Open Source Software

Keywords

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

Repository

Archaeological Time Series - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/aion

Basic Info
Statistics
  • Stars: 10
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 8
Topics
archaeological-science archaeology chronology r-package time-series
Created almost 3 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
```

# aion 


[![status-badge](https://ci.codeberg.org/api/badges/14685/status.svg)](https://ci.codeberg.org/repos/14685){.pkgdown-devel}
[![Code coverage](https://packages.tesselle.org/aion/coverage/badge.svg)](https://packages.tesselle.org/aion/coverage/){.pkgdown-devel}
[![Dependencies](https://tinyverse.netlify.app/badge/aion)](https://cran.r-project.org/package=aion){.pkgdown-devel}

[![r-universe](https://tesselle.r-universe.dev/badges/aion)](https://tesselle.r-universe.dev/aion){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/aion)](https://cran.r-project.org/package=aion){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/aion.svg)](https://cran.r-project.org/web/checks/check_results_aion.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/aion)](https://cran.r-project.org/package=aion){.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 Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.8032278.svg)](https://doi.org/10.5281/zenodo.8032278)
[![DOI JOSS](https://joss.theoj.org/papers/10.21105/joss.06210/status.svg)](https://doi.org/10.21105/joss.06210)


## Overview

Base R ships with a lot of functionality useful for time series, in particular in the **stats** package. However, these features are not adapted to most archaeological time series. These are indeed defined for a given calendar era, they can involve dates very far in the past and the sampling of the observation time is (in most cases) not constant. 

**aion** provides a system of classes and methods to represent and work with such time-series (and time intervals). Dates are represented as *rata die* [@reingold2018], i.e. the number of days since 01-01-01 (Gregorian), with negative values for earlier dates. This allows to represent dates independently of any calendar: it makes calculations and comparisons easier.

Once a time series is created with **aion**, any calendar can be used for printing or plotting data (defaults to Gregorian Common Era; see `vignette("aion")`).

**aion** does not provide tools for temporal modeling. Instead, it offers a simple API that can be used by other specialized packages (see [**kairos**](https://packages.tesselle.org/kairos/) or [**ananke**](https://packages.tesselle.org/ananke/)).

---

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

## Installation

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

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

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/aion")
```

## Usage

```{r load}
## Load package
library(aion)
```

Time-series of ceramic counts:

```{r time-series, fig.width=7, fig.height=7}
## Get ceramic counts (data from Husi 2022)
data("loire", package = "folio")

## Keep only variables whose total is at least 600
keep <- c("01f", "01k", "01L", "08e", "08t", "09b", "15i", "15q")

## Get time midpoints
mid <- rowMeans(loire[, c("lower", "upper")])

## Create time-series
X <- series(
  object = loire[, keep],
  time = mid,
  calendar = AD()
)

## Plot (default calendar)
plot(
  x = X, 
  type = "h" # histogram like vertical lines
)
```

Plot time ranges:

```{r time-intervals, fig.width=7, fig.height=7}
## Create time intervals
Y <- intervals(
  start = loire$lower,
  end = loire$upper,
  names = rownames(loire),
  calendar = AD()
)

## Plot (default calendar)
plot(x = Y)
```

## 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`).

## Related Works

* [**era**](https://github.com/joeroe/era) provides a consistent representation of year-based time scales as a numeric vector with an associated era.

## Contributing

Please note that the **aion** 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.8032278"),
    list(description = "The versioned DOI for version 1.0.0.",
         type = "doi",
         value = "10.5281/zenodo.8032279"),
    list(description = "The versioned DOI for version 1.0.1.",
         type = "doi",
         value = "10.5281/zenodo.8273276"),
    list(description = "The versioned DOI for version 1.0.2.",
         type = "doi",
         value = "10.5281/zenodo.10046426"),
    list(description = "The versioned DOI for version 1.0.3.",
         type = "doi",
         value = "10.5281/zenodo.10926190"),
    list(description = "The versioned DOI for version 1.0.4.",
         type = "doi",
         value = "10.5281/zenodo.12951290"),
    list(description = "The versioned DOI for version 1.1.0.",
         type = "doi",
         value = "10.5281/zenodo.13891247"),
    list(description = "The versioned DOI for version 1.2.0.",
         type = "doi",
         value = "10.5281/zenodo.14144087"),
    list(description = "The versioned DOI for version 1.3.0.",
         type = "doi",
         value = "10.5281/zenodo.14356506"),
    list(description = "The versioned DOI for version 1.4.0.",
         type = "doi",
         value = "10.5281/zenodo.14934480"),
    list(description = "The versioned DOI for version 1.5.0.",
         type = "doi",
         value = "10.5281/zenodo.15305156"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.aion")
  )
)
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

JOSS Publication

aion: An R Package to Represent Archaeological Time Series
Published
April 11, 2024
DOI
Volume 9, Issue 96, Page 6210
Authors
Nicolas Frerebeau ORCID
UMR 6034 Archéosciences Bordeaux, Maison de l'Archéologie, Université Bordeaux Montaigne, 33607 Pessac cedex, France
Editor
Martin Fleischmann ORCID
Tags
archaeology time series chronology
View PDF Review Thread Software Archive

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 "aion" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'aion: Archaeological Time Series'
version: 1.5.0
doi: 10.21105/joss.06210
identifiers:
- description: The concept DOI.
  type: doi
  value: 10.5281/zenodo.8032278
- description: The versioned DOI for version 1.0.0.
  type: doi
  value: 10.5281/zenodo.8032279
- description: The versioned DOI for version 1.0.1.
  type: doi
  value: 10.5281/zenodo.8273276
- description: The versioned DOI for version 1.0.2.
  type: doi
  value: 10.5281/zenodo.10046426
- description: The versioned DOI for version 1.0.3.
  type: doi
  value: 10.5281/zenodo.10926190
- description: The versioned DOI for version 1.0.4.
  type: doi
  value: 10.5281/zenodo.12951290
- description: The versioned DOI for version 1.1.0.
  type: doi
  value: 10.5281/zenodo.13891247
- description: The versioned DOI for version 1.2.0.
  type: doi
  value: 10.5281/zenodo.14144087
- description: The versioned DOI for version 1.3.0.
  type: doi
  value: 10.5281/zenodo.14356506
- description: The versioned DOI for version 1.4.0.
  type: doi
  value: 10.5281/zenodo.14934480
- description: The versioned DOI for version 1.5.0.
  type: doi
  value: 10.5281/zenodo.15305156
- description: The CRAN DOI
  type: doi
  value: 10.32614/cran.package.aion
abstract: A toolkit for archaeological time series and time intervals. This package
  provides a system of classes and methods to represent and work with archaeological
  time series and time intervals. Dates are represented as "rata die" and can be converted
  to (virtually) any calendar defined by Reingold and Dershowitz (2018) <https://doi.org/10.1017/9781107415058>.
  This packages offers a simple API that can be used by other specialized packages.
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
preferred-citation:
  type: article
  title: 'aion: An R Package to Represent Archaeological Time Series'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2024'
  journal: Journal of Open Source Software
  volume: '9'
  issue: '96'
  doi: 10.21105/joss.06210
  start: '6210'
repository: https://CRAN.R-project.org/package=aion
repository-code: https://codeberg.org/tesselle/aion
url: https://packages.tesselle.org/aion/
contact:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
keywords:
- time-series
- r-package
- archaeology
- archaeological-science
- chronology
references:
- type: manual
  title: 'aion: Archaeological Time Series'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
  - family-names: Roe
    given-names: Joe
  year: '2025'
  institution:
    name: Université Bordeaux Montaigne
    address: Pessac, France
  notes: R package version 1.5.0
  url: https://packages.tesselle.org/aion/
  doi: 10.5281/zenodo.8032278
- 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: '>= 3.3'
- 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: '>= 1.10.0'
- type: software
  title: graphics
  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: 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
    affiliation: Université Bordeaux Montaigne
  year: '2025'
  doi: 10.32614/CRAN.package.folio
  version: '>= 1.5.0'
- 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
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  - family-names: Lise
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  year: '2025'
  doi: 10.32614/CRAN.package.svglite
- type: software
  title: tinysnapshot
  abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
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  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

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