Packages

The tesselle packages focus on quantitative analysis methods developed for archaeology. They are designed to work seamlessly together and to complement general-purpose and other specialized statistical packages. These packages can be used to explore and analyze common data types in archaeology: count data, compositional data and chronological data.

Most of our packages are distributed on CRAN, development versions and non-CRAN packages (e.g. WIP packages and large data packages) can be installed from our repository.

Install the complete suite with:

install.packages("tesselle")

Browse the documentation on packages.tesselle.org.

Count data

tabula

An easy way to examine archaeological count data. tabula 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.). The package make it easy to visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams. Read the doc…

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

CRAN Version

DOI JOSS

Compositional data

nexus

Sourcing archaeological materials by chemical composition. nexus allows the exploration and analysis of compositional data in the framework of Aitchison (1986). It provides tools for chemical fingerprinting and source tracking of ancient materials. Initial development is in progress. Read the doc…

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

CRAN Version

Chronological data

kairos

A toolkit for absolute dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site. Read the doc…

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

CRAN Version

chronos

Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from ChronoModel, Oxcal or BCal. This package provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases). Read the doc…

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

CRAN Version

Multivariate data analysis

dimensio

Simple Principal Components Analysis (PCA) and Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984) and Lebart, Piron, and Morineau (2006). Read the doc…

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

CRAN Version

Signal processing

alkahest

A lightweight, dependency-free toolbox for pre-processing XY data from experimental methods (i.e. any signal that can be measured along a continuous variable). This package provides methods for baseline estimation and correction, smoothing, normalization, integration and peaks detection. Read the doc…

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

CRAN Version

Data visualization

khroma

Colour schemes ready for each type of data (qualitative, diverging or sequential), with colours that are distinct for all people, including colour-blind readers. This package provides an implementation of Paul Tol (2018) and Fabio Crameri (2018) colour schemes for use with graphics or ggplot2. It provides tools to simulate colour-blindness and to test how well the colours of any palette are identifiable. Several scientific thematic schemes (geologic timescale, land cover, FAO soils, etc.) are also implemented. Read the doc…

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

CRAN Version

Tools

arkhe

A collection of simple functions for cleaning rectangular data. This package allows to detect, count and replace values or delete rows/columns according to a specific predicate. In addition, it provides tools to check conditions and return informative error messages. Read the doc…

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

CRAN Version

Datasets

folio

Datasets for teaching quantitative approaches and modeling in archaeology and paleontology. folio provides several types of data related to broad topics (cultural evolution, radiocarbon dating, paleoenvironments, etc.), which can be used to illustrate statistical methods in the classroom (multivariate data analysis, compositional data analysis, diversity measurement, etc.). Read the doc…

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

CRAN Version

fasti

Datasets for chronological modelling. This package provides models and data to reproduce results from chronos examples and vignettes. Read the doc…

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

R-universe Version

References

Aitchison, John. 1986. The Statistical Analysis of Compositional Data. Monographs on Statistics and Applied Probability. London: Chapman and Hall. https://doi.org/10.1007/978-94-009-4109-0.
Bertin, Jacques. 1977. La graphique et le traitement graphique de l’information. Nouvelle bibliothèque scientifique. Paris: Flammarion.
Ford, James A. 1962. A Quantitative Method for Deriving Cultural Chronology. Technical Manual 1. Washington, DC: Pan American Union.
Greenacre, Michael J. 1984. Theory and Applications of Correspondence Analysis. London: Academic Press.
Lebart, Ludovic, Marie Piron, and Alain Morineau. 2006. Statistique exploratoire multidimensionnelle : Visualisations et inférences en fouilles de données. Paris: Dunod.