arkhe (version 0.5.0)

coerce: Coerce

Description

Coerces an object to a *Matrix object.

Usage

as_long(from, ...)
as_count(from)
as_composition(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_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)

Value

A coerced object.

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.

Abundance Matrix

The CountMatrix, CompositionMatrix and IncidenceMatrix classes have special slots:

• samples for replicated measurements/observation,

• groups to group data by site/area,

• dates to specify the date point estimate of an assemblage,

• tqp and taq to specify the chronology of an assemblage.

When coercing a data.frame to a *Matrix object, an attempt is made to automatically assign values to these slots by mapping column names (case insensitive, plural insensitive). This behavior can be disabled by setting options(arkhe.autodetect = FALSE) or overrided by explicitly specifying the columns to be used in as_*().

Chronology

The way chronological information is handled is somewhat opinionated. Sub-annual precision is overkill/meaningless in most situations: dates are assumed to be expressed in years CE and are stored as integers (values are coerced with as.integer() and hence truncated towards zero).

Author

N. Frerebeau

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 classes: CompositionMatrix-class, CountMatrix-class, DataMatrix, IncidenceMatrix-class, OccurrenceMatrix-class, StratigraphicMatrix-class

Examples

## Create a count matrix
A0 <- matrix(data = sample(0:10, 100, TRUE), nrow = 20, ncol = 5)

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

## Coerce to relative frequencies
B0 <- 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(B0)
all(A1 == A2)

## Coerce to presence/absence
C0 <- as_incidence(A1)

## Coerce to a co-occurrence matrix
D0 <- as_occurrence(A1)

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

Y <- data.frame(A1)
head(Y)