arkhe (version 0.2.0)

CountMatrix-class: Absolute Frequency Matrix

Description

An S4 class to represent an absolute frequency matrix (i.e. the number of times a given datum occurs in a dataset).

Usage

CountMatrix(data = 0, nrow = 1, ncol = 1, byrow = FALSE,
  dimnames = NULL, ...)

Arguments

data

an optional data vector (including a list or expression vector). Non-atomic classed R objects are coerced by as.vector and all attributes discarded.

nrow

the desired number of rows.

ncol

the desired number of columns.

byrow

logical. If FALSE (the default) the matrix is filled by columns, otherwise the matrix is filled by rows.

dimnames

A dimnames attribute for the matrix: NULL or a list of length 2 giving the row and column names respectively. An empty list is treated as NULL, and a list of length one as row names. The list can be named, and the list names will be used as names for the dimensions.

...

additional arguments to be passed to or from methods.

Matrix ID

When a matrix is first created, an identifier is generated (UUID v4). This ID is preserved when coercing to another class. Thus, the object ID is unique within the same class, but two objects of different classes can have the same ID. This makes it possible to identify objects representing the same initial data and associate them with the results of specific computations.

Get and set

In the code snippets below, x is a *Matrix object.

get_id(x)

Get the ID of x.

get_dates(x) and set_dates(x) <- value

Get or set the dates of x.

get_coordinates(x) and set_coordinates(x) <- value

Get or set the geographical coordinates of x.

Access

In the code snippets below, x is a *Matrix object.

dim(x)

Returns the dimension of x.

nrow(x)

Returns the number of rows present in x.

ncol(x)

Returns the number of columns present in x.

dimnames(x), dimnames(x) <- value

Retrieves or sets the row dimnames of x according to value.

rownames(x), rownames(x) <- value

Retrieves or sets the row names of x according to value.

colnames(x), colnames(x) <- value

Retrieves or sets the column names of x according to value.

Subset

In the code snippets below, x is a *Matrix object.

x[i, j]

Extracts elements selected by subscripts i and j. Indices are numeric, integer or character vectors or empty (missing) or NULL. Numeric values are coerced to integer as by as.integer (and hence truncated towards zero). Character vectors will be matched to the name of the elements. An empty index (a comma separated blank) indicates that all entries in that dimension are selected. Returns an object of the same class as x.

x[[i]]

Extracts a single element selected by subscript i.

See Also

'>NumericMatrix

Other matrix: AbundanceMatrix-class, IncidenceMatrix-class, LogicalMatrix-class, Matrix-class, NumericMatrix-class, OccurrenceMatrix-class, SimilarityMatrix-class, StratigraphicMatrix-class, coerce

Examples

# NOT RUN {
## Create a count data matrix
A1 <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 10, ncol = 10)

## Access
get_id(A1)
dim(A1) # Get the matrix dimensions
colnames(A1) <- letters[11:20] # Set the column names
colnames(A1) # Get the column names
rownames(A1) <- LETTERS[1:10] # Set the row names
rownames(A1) # Get the rownames

## Subset
A1[[1]] # Get the first value
A1[, ] # Get all values
A1[1, ] # Get the first row
A1[c("A", "B", "C"), ] # Get the first three rows
A1[c("A", "B", "C"), 1] # Get the first three rows of the first column
A1[, 1, drop = FALSE] # Get the first column

## Coerce counts to relative frequencies
B <- as_abundance(A1)
## Row sums are internally stored before coercing to a frequency matrix
get_totals(B) # Get row sums
## This allows to restore the source data
A2 <- as_count(B)
all(A1 == A2)
## Coerce to a co-occurrence matrix
B <- as_occurrence(A1)
# }