tabula

tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data - Published in JOSS (2019)

https://github.com/tesselle/tabula

Keywords

archaeological-science archaeology data-visualization r-package

Scientific Fields

Biology Life Sciences - 60% confidence

Engineering Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Analysis and Visualization of Archaeological Count Data - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/tabula

Basic Info

Host: GitHub
Owner: tesselle
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://packages.tesselle.org/tabula/
Size: 16.3 MB

Statistics

Stars: 36
Watchers: 5
Forks: 6
Open Issues: 0
Releases: 18

Topics

archaeological-science archaeology data-visualization r-package

Created about 7 years ago · Last pushed 4 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
```

# tabula 


[![status-badge](https://ci.codeberg.org/api/badges/14696/status.svg)](https://ci.codeberg.org/repos/14696){.pkgdown-devel}
[![Code coverage](https://packages.tesselle.org/tabula/coverage/badge.svg)](https://packages.tesselle.org/tabula/coverage/){.pkgdown-devel}
[![Dependencies](https://tinyverse.netlify.app/badge/tabula)](https://cran.r-project.org/package=tabula){.pkgdown-devel}

[![r-universe](https://tesselle.r-universe.dev/badges/tabula)](https://tesselle.r-universe.dev/tabula){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/tabula)](https://cran.r-project.org/package=tabula){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/tabula.svg)](https://cran.r-project.org/web/checks/check_results_tabula.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/tabula)](https://cran.r-project.org/package=tabula){.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.1489944.svg)](https://doi.org/10.5281/zenodo.1489944)
[![DOI JOSS](https://joss.theoj.org/papers/10.21105/joss.01821/status.svg)](https://doi.org/10.21105/joss.01821)


## Overview

An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, @ford1962 and @bertin1977 diagrams, etc. **tabula** provides methods for:

* Diversity measurement: `diversity()`, `heterogeneity()`, `evenness()`, `richness()`, `rarefaction()`, `turnover()`.
* Similarity measurement and co-occurrence: `similarity()`, `occurrence()`.
* Assessing sample size and significance: `bootstrap()`, `jackknife()`, `simulate()`.
* @bertin1977 or @ford1962 (battleship curve) diagrams: `plot_bertin()`, `plot_ford()`.
* Seriograph [@desachy2004]: `seriograph()`, `matrigraph()`.
* Heatmaps: `plot_heatmap()`, `plot_spot()`.

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

---

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

## Installation

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

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

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/tabula")
```

## Usage

```{r packages-load, message=FALSE}
## Install extra packages (if needed)
# install.packages("folio")

## Load the package
library(tabula)
```

*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 ford, fig.width=8, fig.height=7, fig.align="center"}
## Data from Lipo et al. 2015
data("mississippi", package = "folio")

## Ford diagram
plot_ford(mississippi)
```

```{r occurrence, fig.width=7, fig.height=7, fig.align="center"}
## Co-occurrence of ceramic types
mississippi |> 
  occurrence() |> 
  plot_spot()
```

```{r sample-size, fig.width=5, fig.height=5, fig.show="hold", out.width='50%'}
## Data from Conkey 1980, Kintigh 1989, p. 28
data("chevelon", package = "folio")

## Measure diversity by comparing to simulated assemblages
chevelon |>
  heterogeneity(method = "shannon") |>
  simulate(seed = 12345) |>
  plot()

chevelon |>
  richness(method = "count") |>
  simulate(seed = 12345) |>
  plot()
```

## 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 **tabula** 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.1489944"),
    list(description = "The versioned DOI for version 0.9.0.",
         type = "doi",
         value = "10.5281/zenodo.1489945"),
    list(description = "The versioned DOI for version 1.0.0.",
         type = "doi",
         value = "10.5281/zenodo.1881131"),
    list(description = "The versioned DOI for version 1.1.0.",
         type = "doi",
         value = "10.5281/zenodo.2529084"),
    list(description = "The versioned DOI for version 1.2.0.",
         type = "doi",
         value = "10.5281/zenodo.2600844"),
    list(description = "The versioned DOI for version 1.3.0.",
         type = "doi",
         value = "10.5281/zenodo.3455385"),
    list(description = "The versioned DOI for version 1.4.0.",
         type = "doi",
         value = "10.5281/zenodo.3552904"),
    list(description = "The versioned DOI for version 1.5.0.",
         type = "doi",
         value = "10.5281/zenodo.3612110"),
    list(description = "The versioned DOI for version 1.5.1.",
         type = "doi",
         value = "10.5281/zenodo.3716163"),
    list(description = "The versioned DOI for version 1.6.0.",
         type = "doi",
         value = "10.5281/zenodo.4748807"),
    list(description = "The versioned DOI for version 1.6.1.",
         type = "doi",
         value = "10.5281/zenodo.4793496"),
    list(description = "The versioned DOI for version 1.7.0.",
         type = "doi",
         value = "10.5281/zenodo.6703727"),
    list(description = "The versioned DOI for version 1.8.0.",
         type = "doi",
         value = "10.5281/zenodo.7060361"),
    list(description = "The versioned DOI for version 2.0.0.",
         type = "doi",
         value = "10.5281/zenodo.7296619"),
    list(description = "The versioned DOI for version 3.0.0.",
         type = "doi",
         value = "10.5281/zenodo.8274042"),
    list(description = "The versioned DOI for version 3.0.1.",
         type = "doi",
         value = "10.5281/zenodo.10214364"),
    list(description = "The versioned DOI for version 3.1.0.",
         type = "doi",
         value = "10.5281/zenodo.11205411"),
    list(description = "The versioned DOI for version 3.1.1.",
         type = "doi",
         value = "10.5281/zenodo.13711170"),
    list(description = "The versioned DOI for version 3.2.0.",
         type = "doi",
         value = "10.5281/zenodo.14632153"),
    list(description = "The versioned DOI for version 3.2.1.",
         type = "doi",
         value = "10.5281/zenodo.15124670"),
    list(description = "The versioned DOI for version 3.3.0.",
         type = "doi",
         value = "10.5281/zenodo.15397990"),
    list(description = "The versioned DOI for version 3.3.1.",
         type = "doi",
         value = "10.5281/zenodo.15425370"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.tabula")
  )
)
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

Website: www.tesselle.org
Repositories: 5
Profile: https://github.com/tesselle

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 "tabula" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'tabula: Analysis and Visualization of Archaeological Count Data'
version: 3.3.1
doi: 10.21105/joss.01821
identifiers:
- description: The concept DOI.
  type: doi
  value: 10.5281/zenodo.1489944
- description: The versioned DOI for version 0.9.0.
  type: doi
  value: 10.5281/zenodo.1489945
- description: The versioned DOI for version 1.0.0.
  type: doi
  value: 10.5281/zenodo.1881131
- description: The versioned DOI for version 1.1.0.
  type: doi
  value: 10.5281/zenodo.2529084
- description: The versioned DOI for version 1.2.0.
  type: doi
  value: 10.5281/zenodo.2600844
- description: The versioned DOI for version 1.3.0.
  type: doi
  value: 10.5281/zenodo.3455385
- description: The versioned DOI for version 1.4.0.
  type: doi
  value: 10.5281/zenodo.3552904
- description: The versioned DOI for version 1.5.0.
  type: doi
  value: 10.5281/zenodo.3612110
- description: The versioned DOI for version 1.5.1.
  type: doi
  value: 10.5281/zenodo.3716163
- description: The versioned DOI for version 1.6.0.
  type: doi
  value: 10.5281/zenodo.4748807
- description: The versioned DOI for version 1.6.1.
  type: doi
  value: 10.5281/zenodo.4793496
- description: The versioned DOI for version 1.7.0.
  type: doi
  value: 10.5281/zenodo.6703727
- description: The versioned DOI for version 1.8.0.
  type: doi
  value: 10.5281/zenodo.7060361
- description: The versioned DOI for version 2.0.0.
  type: doi
  value: 10.5281/zenodo.7296619
- description: The versioned DOI for version 3.0.0.
  type: doi
  value: 10.5281/zenodo.8274042
- description: The versioned DOI for version 3.0.1.
  type: doi
  value: 10.5281/zenodo.10214364
- description: The versioned DOI for version 3.1.0.
  type: doi
  value: 10.5281/zenodo.11205411
- description: The versioned DOI for version 3.1.1.
  type: doi
  value: 10.5281/zenodo.13711170
- description: The versioned DOI for version 3.2.0.
  type: doi
  value: 10.5281/zenodo.14632153
- description: The versioned DOI for version 3.2.1.
  type: doi
  value: 10.5281/zenodo.15124670
- description: The versioned DOI for version 3.3.0.
  type: doi
  value: 10.5281/zenodo.15397990
- description: The versioned DOI for version 3.3.1.
  type: doi
  value: 10.5281/zenodo.15425370
- description: The CRAN DOI
  type: doi
  value: 10.32614/cran.package.tabula
abstract: 'An easy way to examine archaeological count data. This package provides
  several tests and measures of diversity: heterogeneity and evenness (Brillouin,
  Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.),
  turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize
  count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962)
  and Bertin (1977) diagrams, etc.'
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: article
  title: 'tabula: An R Package for Analysis, Seriation, and Visualization of 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: '2019'
  journal: Journal of Open Source Software
  volume: '4'
  issue: '44'
  doi: 10.21105/joss.01821
  start: '1821'
repository: https://CRAN.R-project.org/package=tabula
repository-code: https://codeberg.org/tesselle/tabula
url: https://packages.tesselle.org/tabula/
contact:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
keywords:
- archaeological-science
- archaeology
- data-visualization
- diversity-index
- r-package
references:
- type: manual
  title: 'tabula: Analysis and Visualization of Archaeological Count Data'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
  year: '2025'
  institution:
    name: Université Bordeaux Montaigne
    address: Pessac, France
  notes: R package version 3.3.1
  url: https://packages.tesselle.org/tabula/
  doi: 10.5281/zenodo.1489944
- 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: 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: 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: khroma
  abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
  notes: Imports
  url: https://packages.tesselle.org/khroma/
  repository: https://CRAN.R-project.org/package=khroma
  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.khroma
  version: '>= 1.16.0'
- 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: 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: 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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GitHub Events

Total

Release event: 1
Watch event: 1
Push event: 17
Fork event: 1
Create event: 4

Last Year

Release event: 1
Watch event: 1
Push event: 17
Fork event: 1
Create event: 4

Committers

Last synced: 5 months ago

All Time

Total Commits: 705
Total Committers: 3
Avg Commits per committer: 235.0
Development Distribution Score (DDS): 0.004

Past Year

Commits: 50
Committers: 1
Avg Commits per committer: 50.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
nfrerebeau	3****u	702
Ben Marwick	b**k@h**m	2
soodoku	g**7@g**m	1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 20
Total pull requests: 6
Average time to close issues: 20 days
Average time to close pull requests: 7 days
Total issue authors: 7
Total pull request authors: 4
Average comments per issue: 1.05
Average comments per pull request: 0.5
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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nfrerebeau (10)
soodoku (5)
akarlinsky (1)
tsdye (1)
jayrobwilliams (1)
benmarwick (1)
airesarch (1)

ecosyste.ms

Data

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Open Source Science

tabula

Science Score: 67.0%

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Scientific Fields

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Citation (CITATION.cff)

CodeMeta (codemeta.json)

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