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README.Rmd
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README.Rmd
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---
output: github_document
bibliography: vignettes/bibliography.bib
nocite: '@*'
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = NULL
)
Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
```
# tabula <img width=120px src="man/figures/logo.png" align="right" />
<!-- badges: start -->
[](https://github.com/tesselle/tabula/actions)
[](https://app.codecov.io/gh/tesselle/tabula)
[](https://www.codefactor.io/repository/github/tesselle/tabula)
[](https://cran.r-project.org/package=tabula)
[](https://tesselle.r-universe.dev/tabula){.pkgdown-devel}
[](https://cran.r-project.org/package=tabula){.pkgdown-release}
[](https://cran.r-project.org/web/checks/check_results_tabula.html){.pkgdown-release}
[](https://cran.r-project.org/package=tabula){.pkgdown-release}
[](https://www.repostatus.org/#active)
[](https://doi.org/10.5281/zenodo.1489944)
[](https://doi.org/10.21105/joss.01821)
<!-- badges: end -->
## 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: `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 [GitHub](https://github.com/) with:
```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_github("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", out.width='100%'}
## 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
set.seed(12345)
chevelon |>
heterogeneity(method = "shannon") |>
simulate() |>
plot()
chevelon |>
richness(method = "count") |>
simulate() |>
plot()
```
## 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