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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:

Diversity measurement: heterogeneity(), evenness(), richness(),
rarefaction(), turnover().
Similarity measurement and co-occurrence: similarity(),
occurrence().
Assessing sample size and significance: bootstrap(), jackknife(),
simulate().
Bertin (1977) or Ford (1962) (battleship curve) diagrams:
plot_bertin(), plot_ford().
Seriograph (Desachy 2004): seriograph(), matrigraph().
Heatmaps: plot_heatmap(), plot_spot().

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).
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 3.2.0,
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 GitHub with:

# install.packages("remotes")
remotes::install_github("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
set.seed(12345)
chevelon |>
  heterogeneity(method = "shannon") |>
  simulate() |>
  plot()
chevelon |>
  richness(method = "count") |>
  simulate() |>
  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.

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