arkhe (version 0.5.0)

OccurrenceMatrix-class: Co-Occurrence Matrix

Description

An S4 class to represent a co-occurrence matrix.

Slots

total

An integer giving the total number of observations.

Author

N. Frerebeau

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.

See Also

as_occurrence()

Other classes: CompositionMatrix-class, CountMatrix-class, DataMatrix, IncidenceMatrix-class, StratigraphicMatrix-class, coerce()

Examples

## 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