arkhe (version 0.5.0)

subset: Extract or Replace Parts of an Object

Description

Operators acting on objects to extract or replace parts.

Usage

# S4 method for AbundanceMatrix
[(x, i, j, ..., drop = TRUE)
# S4 method for AbundanceMatrix
[(x, i, j, ...) <- value
# S4 method for AbundanceMatrix
[[(x, i, j, ...) <- value

Value

A subsetted object of the same sort as x.

Arguments

x

An object from which to extract element(s) or in which to replace element(s) (typically a *Matrix object).

i, j

Indices specifying elements to extract or replace. 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.

...

Currently not used.

drop

A logical scalar: should the result be coerced to the lowest possible dimension? This only works for extracting elements, not for the replacement.

value

A possible value for the element(s) of x.

Author

N. Frerebeau

See Also

Other mutators: mutators, summary()

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