transform_clr function

Centered Log-Ratios (CLR)

Computes CLR transformation. methods

transform_clr(object, ...)

## S4 method for signature 'CompositionMatrix'
transform_clr(object, weights = FALSE)

## S4 method for signature 'GroupedComposition'
transform_clr(object, weights = FALSE)

## S4 method for signature 'ALR'
transform_clr(object)

## S4 method for signature 'GroupedALR'
transform_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 $1$).

Returns

A CLR object.

Details

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

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)

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()

Author(s)

N. Frerebeau