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An S4 class to represent an incidence (presence/absence) matrix.
IncidenceMatrix(
data = FALSE,
nrow = 1,
ncol = 1,
byrow = FALSE,
dimnames = NULL,
...
)
an optional data vector (including a list or
expression
vector). Non-atomic classed R objects are
coerced by as.vector
and all attributes discarded.
the desired number of rows.
the desired number of columns.
logical. If FALSE
(the default) the matrix is
filled by columns, otherwise the matrix is filled by rows.
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.
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.
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
.
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
.
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
.
Other matrix:
AbundanceMatrix-class
,
CountMatrix-class
,
LogicalMatrix-class
,
Matrix-class
,
NumericMatrix-class
,
OccurrenceMatrix-class
,
SimilarityMatrix-class
,
StratigraphicMatrix-class
,
coerce()
# NOT RUN {
## 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 = 10)
## Create a count data matrix
B <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 10)
## Coerce to presence/absence
C <- as_incidence(B)
# }
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