# OccurrenceMatrix-class: Co-Occurrence Matrix In arkhe: Representation of Archaeological Data

## Description

An S4 class to represent a co-occurrence matrix.

## Details

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

## Slots

`total`

An `integer` giving the total number of observations.

## Author(s)

N. Frerebeau

`as_occurrence()`
Other classes: `CompositionMatrix-class`, `CountMatrix-class`, `DataMatrix`, `IncidenceMatrix-class`, `StratigraphicMatrix-class`, `coerce()`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24``` ```## Create an incidence (presence/absence) matrix ## Data will be coerced with as.logical() A <- IncidenceMatrix(data = sample(0:1, 100, TRUE, c(1, 1/3)), nrow = 20) ## Create a count data matrix B <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 20) ## Access dim(B) # Get the matrix dimensions row(B) # Get the row indexes col(B, as.factor = TRUE) # Get the column indexes nrow(B) # Get the number of rows ncol(B) # Get the number of columns dimnames(B) # Get the dimension names rownames(B) <- LETTERS[1:20] # Set the row names rownames(B) # Get the rownames colnames(B) <- letters[21:25] # Set the column names colnames(B) # Get the column names ## Subset B[[1, 1]] # Get the first value B[1] # Get the first value B[, ] # Get all values B[1, , drop = FALSE] # Get the first row B[, 1:3] # Get the first three column ```