README.md

tabula

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r-universe CRAN Version CRAN checks CRAN Downloads

Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.

DOI
Zenodo DOI
JOSS

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, Ford (1962) and Bertin (1977) diagrams, etc. tabula provides methods for:

kairos is a companion package to tabula that provides functions for chronological modeling and dating of archaeological assemblages from count data.

To cite tabula in publications use:

Frerebeau N (2019). “tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data.” Journal of Open Source Software, 4(44), 1821. https://doi.org/10.21105/joss.01821.

Frerebeau N (2025). tabula: Analysis and Visualization of Archaeological Count Data. Université Bordeaux Montaigne, Pessac, France. https://doi.org/10.5281/zenodo.1489944, R package version 3.3.1, https://packages.tesselle.org/tabula/.

This package is a part of the tesselle project https://www.tesselle.org.

Installation

You can install the released version of tabula from CRAN with:

install.packages("tabula")

And the development version from Codeberg with:

# install.packages("remotes")
remotes::install_git("https://codeberg.org/tesselle/tabula")

Usage

## 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.

## Data from Lipo et al. 2015
data("mississippi", package = "folio")

## Ford diagram
plot_ford(mississippi)

## Co-occurrence of ceramic types
mississippi |> 
  occurrence() |> 
  plot_spot()

## 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):

Sys.setenv(LANGUAGE = "<language code>")

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

Contributing

Please note that the tabula project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

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