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

DOI

Overview

A collection of classes that represent archaeological data. This package provides a set of S4 classes that extend the basic matrix data type (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.

Installation

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

Or install the development version from GitHub with:

Usage

# See the vignette
utils::vignette("arkhe", package = "arkhe")

arkhe provides a set of S4 classes that extend the basic matrix data type. These new classes represent different special types of matrix.

  • Numeric matrix:
    • CountMatrix represents absolute frequency data,
    • AbundanceMatrix represents relative frequency data,
    • OccurrenceMatrix represents a co-occurrence matrix,
    • SimilarityMatrix represents a (dis)similarity matrix,
  • Logical matrix:
    • IncidenceMatrix represents presence/absence data,
    • StratigraphicMatrix represents stratigraphic relationships.

It assumes that you keep your data tidy: each variable (type/taxa) must be saved in its own column and each observation (assemblage/sample) must be saved in its own row.

These new classes are of simple use, on the same way as the base matrix:

arkhe uses coercing mechanisms (with validation methods) for data type conversions:

Represent stratigraphic relationships:

Contributing

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