A collection of classes that represent archaeological data. This package provides a set of S4 classes that represent different special types of matrix (absolute/relative frequency, presence/absence data, co-occurrence matrix, etc.) upon which package developers can build subclasses. It also provides a set of generic methods (mutators and coercion mechanisms) and functions (e.g. predicates). In addition, a few classes of general interest (e.g. that represent stratigraphic relationships) are implemented.
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 Michael J. Greenacre1 and Ludovic Lebart, Marie Piron, and Alain Morineau.2
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.).
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 (e.g. Mean Ceramic Date) and density estimates of the occupation and duration of an archaeological site.
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
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.
Sourcing archaeological materials by chemical composition. nexus allows the exploration and analysis of compositional data in the framework of John Aitchison.3 It provides tools for chemical fingerprinting and source tracking of ancient materials. Initial development is in progress.
An easy way to examine archaeological count data. tabula provides a convenient and reproducible toolkit for relative dating by matrix seriation (reciprocal ranking, CA-based seriation). The 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.). The package make it easy to visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, James A. Ford4 and Jacques Bertin5 diagrams.