Coerce

Coerce

as_long(from, ...)

as_count(from)

as_composition(from)

as_abundance(from)

as_incidence(from)

as_occurrence(from)

as_features(from)

as_stratigraphy(from)

# S4 method for ANY
as_count(from)

# S4 method for ANY
as_composition(from)

# S4 method for ANY
as_abundance(from)

# S4 method for ANY
as_incidence(from)

# S4 method for ANY
as_occurrence(from)

# S4 method for ANY
as_stratigraphy(from)

# S4 method for matrix
as_long(from, factor = FALSE, reverse = FALSE)

# S4 method for AbundanceMatrix
as_long(from, factor = FALSE, reverse = FALSE)

# S4 method for AbundanceMatrix
as_features(from)

Arguments

from	An object to be coerced.
...	Currently not used.
factor	A logical scalar: should character string be coerced to factor? Default to FALSE, if TRUE the original ordering is preserved.
reverse	A logical scalar: should the order of factor levels be reversed? Only used if factor is TRUE. Useful for plotting.

Value

A coerced object.

Details

The following methods coerce an object to a *Matrix object:

Method	Target	Details
as_count()	CountMatrix	absolute frequency data
as_composition()	CompositionMatrix	relative frequency data
as_incidence()	IncidenceMatrix	presence/absence data
as_occurrence()	OccurrenceMatrix	co-occurrence
as_stratigraphy()	StratigraphicMatrix	stratigraphic relationships

Note that as_count rounds numeric values to zero decimal places and then coerces to integer as by as.integer().

as_stratigraphy() converts a set of stratigraphic relationships (edges) to a stratigraphic (adjacency) matrix. from can be a matrix, list, or data.frame: the first column/component is assumed to contain the bottom units and the second the top units (adjacency).

Method	Target	Details
as_long()	data.frame	long S3 data frame
as_features()	data.frame	wide S3 data frame

as_features() converts a *Matrix object to a collection of features: a data.frame with all informations as extra columns (result may differ according to the class of from).

See also

Other matrix: CompositionMatrix-class, CountMatrix-class, DataMatrix, IncidenceMatrix-class, OccurrenceMatrix-class, StratigraphicMatrix-class

Author

N. Frerebeau

Examples

## Create a count matrix
A0 <- matrix(data = sample(0:10, 100, TRUE), nrow = 10, ncol = 5)

## Coerce to absolute frequencies
A1 <- as_count(A0)

## Coerce to relative frequencies
B <- as_composition(A1)

## Row sums are internally stored before coercing to relative frequencies
## (use get_totals() to retrieve these values)
## This allows to restore the source data
A2 <- as_count(B)
all(A1 == A2)
#> [1] TRUE

## Coerce to presence/absence
C <- as_incidence(A1)

## Coerce to a co-occurrence matrix
D <- as_occurrence(A1)

## Coerce to an S3 matrix or data.frame
X <- as.matrix(A1)
all(A0 == X)
#> [1] TRUE

Y <- data.frame(A1)
head(Y)
#>      col1 col2 col3 col4 col5
#> row1   10   10    1    9    1
#> row2    9    0    3    7    5
#> row3    3    4    9    0   10
#> row4    7    1    7    1    0
#> row5    6    8    6    3    2
#> row6    6    0    3    0    1

## Collection of features
# set_dates(A1) <- matrix(sample(0:10, 20, TRUE), nrow = 10, ncol = 2)
# set_coordinates(A1) <- matrix(sample(0:10, 30, TRUE), nrow = 10, ncol = 3)
# as_features(A1)