Manual

N. Frerebeau

2020-02-14

1 Definitions

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

It assumes that you keep your data tidy: each variable (taxon/type) must be saved in its own column and each observation (assemblage/sample) must be saved in its own row. Note that missing values are not allowed.

The internal structure of S4 classes implemented in arkhe is depicted in the UML class diagram in the following figure.

1.1 Numeric matrix

1.1.1 Absolute frequency matrix (CountMatrix)

We denote the \(m \times p\) count matrix by \(A = \left[ a_{ij} \right] ~\forall i \in \left[ 1,m \right], j \in \left[ 1,p \right]\) with row and column sums:

\[\begin{align} a_{i \cdot} = \sum_{j = 1}^{p} a_{ij} && a_{\cdot j} = \sum_{i = 1}^{m} a_{ij} && a_{\cdot \cdot} = \sum_{i = 1}^{m} \sum_{j = 1}^{p} a_{ij} && \forall a_{ij} \in \mathbb{N} \end{align}\]

1.1.2 Relative frequency matrix (AbundanceMatrix)

A frequency matrix represents relative abundances.

We denote the \(m \times p\) frequency matrix by \(B = \left[ b_{ij} \right] ~\forall i \in \left[ 1,m \right], j \in \left[ 1,p \right]\) with row and column sums:

\[\begin{align} b_{i \cdot} = \sum_{j = 1}^{p} b_{ij} = 1 && b_{\cdot j} = \sum_{i = 1}^{m} b_{ij} && b_{\cdot \cdot} = \sum_{i = 1}^{m} \sum_{j = 1}^{p} b_{ij} && \forall b_{ij} \in \left[ 0,1 \right] \end{align}\]

1.1.3 Co-occurrence matrix (OccurrenceMatrix)

A co-occurrence matrix is a symmetric matrix with zeros on its main diagonal, which works out how many times (expressed in percent) each pairs of taxa occur together in at least one sample.

The \(p \times p\) co-occurrence matrix \(D = \left[ d_{i,j} \right] ~\forall i,j \in \left[ 1,p \right]\) is defined over an \(m \times p\) abundance matrix \(A = \left[ a_{x,y} \right] ~\forall x \in \left[ 1,m \right], y \in \left[ 1,p \right]\) as:

\[ d_{i,j} = \sum_{x = 1}^{m} \bigcap_{y = i}^{j} a_{xy} \]

with row and column sums:

\[\begin{align} d_{i \cdot} = \sum_{j \geqslant i}^{p} d_{ij} && d_{\cdot j} = \sum_{i \leqslant j}^{p} d_{ij} && d_{\cdot \cdot} = \sum_{i = 1}^{p} \sum_{j \geqslant i}^{p} d_{ij} && \forall d_{ij} \in \mathbb{N} \end{align}\]

1.2 Logical matrix

1.2.1 Incidence matrix (IncidenceMatrix)

We denote the \(m \times p\) incidence matrix by \(C = \left[ c_{ij} \right] ~\forall i \in \left[ 1,m \right], j \in \left[ 1,p \right]\) with row and column sums:

\[\begin{align} c_{i \cdot} = \sum_{j = 1}^{p} c_{ij} && c_{\cdot j} = \sum_{i = 1}^{m} c_{ij} && c_{\cdot \cdot} = \sum_{i = 1}^{m} \sum_{j = 1}^{p} c_{ij} && \forall c_{ij} \in \lbrace 0,1 \rbrace \end{align}\]

2 Usage

# Load packages
library(arkhe)

2.1 Create

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

Note that an AbundanceMatrix can only be created by coercion (see below).

2.2 Coerce

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