nexus (version 0.3.0)

transform_clr: Centered Log-Ratios (CLR)

Description

Computes CLR transformation.

Usage

transform_clr(object, ...)
# S4 method for CompositionMatrix
transform_clr(object, weights = FALSE)
# S4 method for ALR
transform_clr(object)

Value

A CLR object.

Arguments

object

A CompositionMatrix object.

...

Currently not used.

weights

A logical scalar: should varying weights (column means) be used? If FALSE (the default), equally-weighted parts are used. Alternatively, a positive numeric vector of weights can be specified (will be rescaled to sum to \(1\)).

Author

N. Frerebeau

Details

The CLR transformation computes the log of each part relative to the geometric mean of all parts.

References

Aitchison, J. (1986). The Statistical Analysis of Compositional Data. London: Chapman and Hall.

Greenacre, M. J. (2019). Compositional Data Analysis in Practice. Boca Raton: CRC Press.

Greenacre, M. J. (2021). Compositional Data Analysis. Annual Review of Statistics and Its Application, 8(1): 271-299. tools:::Rd_expr_doi("10.1146/annurev-statistics-042720-124436").

See Also

Other log-ratio transformations: transform_alr(), transform_ilr(), transform_inverse(), transform_lr(), transform_plr()

Examples

## Data from Aitchison 1986
data("hongite")

## Coerce to compositional data
coda <- as_composition(hongite)

## Centered log-ratio
clr <- transform_clr(coda)

## Inverse transformation
inv_clr <- transform_inverse(clr)
all.equal(coda, inv_clr)