arkhe

Overview

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.

Installation

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

install.packages("arkhe")

And the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("tesselle/arkhe")

Usage

## Load the package
library(arkhe)

arkhe provides a set of S4 classes that represent different special types of matrix.

• Integer matrix:
  • CountMatrix represents absolute frequency data,
  • OccurrenceMatrix represents a co-occurrence matrix,
• Numeric matrix:
  • CompositionMatrix represents relative frequency (compositional) data,
• 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 as they inherit from the base matrix:

## Define a count data matrix
## (data will be rounded to zero decimal places, then coerced with as.integer)
quanti <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 10, ncol = 10)

## Define a logical matrix
## (data will be coerced with as.logical)
quali <- IncidenceMatrix(data = sample(0:1, 100, TRUE), nrow = 10, ncol = 10)

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

## Create a count matrix
X <- matrix(data = sample(0:10, 75, TRUE), nrow = 15, ncol = 5)

## Coerce to absolute frequencies
A1 <- as_count(X)

## Coerce to relative frequencies
B <- as_composition(A1)

## Row sums are internally stored before coercing to a frequency matrix
## (use get_totals() to get these values)
## This allows to restore the source data
A2 <- as_count(B)
all(A1 == A2)
#> [1] TRUE

## Coerce to presence/absence
D <- as_incidence(A1)

## Coerce to a co-occurrence matrix
E <- as_occurrence(A1)

The CountMatrix, CompositionMatrix and IncidenceMatrix classes have two special slots:

• samples for replicated measurements/observation,
• groups to group data by site/area.

When coercing a data.frame to a *Matrix object, an attempt is made to automatically assign the corresponding values. This behavior can be disabled by setting options(arkhe.autodetect = FALSE).

Y <- as.data.frame(X)
Y$samples <- rep(c("a", "b", "c", "d", "e"), each = 3)
Y$groups <- rep(c("A", "B", "C"), each = 5)

## Coerce to a count matrix
Z <- as_count(Y)

## Get groups
get_samples(Z)
#>  [1] "a" "a" "a" "b" "b" "b" "c" "c" "c" "d" "d" "d" "e" "e" "e"

## Get groups
get_groups(Z)
#>  [1] "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "C" "C" "C" "C" "C"

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.