as_composition function

Coerce to a Closed Compositional Matrix

Coerces an object to a CompositionMatrix object. methods

as_composition(from, ...)

## S4 method for signature 'numeric'
as_composition(from)

## S4 method for signature 'matrix'
as_composition(from)

## S4 method for signature 'data.frame'
as_composition(
  from,
  parts = NULL,
  groups = NULL,
  autodetect = TRUE,
  verbose = getOption("nexus.verbose")
)

Arguments

• from: A matrix or data.frame to be coerced.
• ...: Currently not used.
• parts: A vector giving the index of the column to be used a compositional parts. If NULL and autodetect is TRUE (the default), all numeric columns will be used.
• groups: An integer giving the index of the column to be used to group the samples. If NULL (the default), no grouping is stored.
• autodetect: A logical scalar: should numeric variables be automatically used as compositional parts?
• verbose: A logical scalar: should report extra information on progress?

Returns

A CompositionMatrix object.

Details

See vignette("nexus").

Examples

## Create a count matrix
A1 <- matrix(data = sample(1:100, 100, TRUE), nrow = 20)

## Coerce to compositions
B <- as_composition(A1)

## Row sums are internally stored before coercing to relative frequencies
totals(B)

## This allows to restore the source data
A2 <- as_amounts(B)

## Coerce to a data.frame
X <- as.data.frame(B)
head(X)

See Also

Other compositional data tools: as_amounts()

Author(s)

N. Frerebeau