rgr (version 1.1.15)

clr: Centred Log-Ratio (clr) transformation

Description

Undertakes a centred log-ratio transformation to remove the effects of closure in a data matrix.

Usage

clr(xx, ifclose = FALSE, ifwarn = TRUE)

Arguments

xx

a n by p matrix to be log centred. It is essential that a single unit of measurement is used. Thus it may be required to convert, for example, determinations in percent to ppm (mg/kg) so that all measurements are in ppm prior to executing this function. Natural logarithms are used.

ifclose

if it is required to close a data set prior to transformation set ifclose = TRUE.

ifwarn

by default ifwarn = TRUE which generates a reminder/warning that when carrying out a centred log-ratio transformation all the data/parts must be in the same measurement units. The message can be suppressed by setting ifwarn = FALSE.

Value

x

a n by p matrix of log-centred values.

Details

Most analytical chemical data for major, minor and trace elements are of a closed form, i.e. for a physical individual sample they sum to a constant, whether it be percent, ppm (mg/kg), or some other units. It does not matter that only some components contributing to the constant sum are present in the matrix, the data are closed. As a result, as some elements increase in concentration others must decrease, this leads to correlation measures and graphical presentations that do not reflect the true underlying relationships. A centred log-ratio is one procedure for removing closure effects, others are additive log-ratios (alr) and isometric log-ratios (ilr).

References

Aitchison, J., 1984. The statistical analysis of geochemical compositions. Mathematical Geology, 16(6):531-564.

Aitchison, J., 1986. The Statistical Analysis of Compositional data. Chapman and Hall, London, U.K., 416 p.

Aitchison, J. and Egozcue, J.J., 2005. Compositional data analysis; where are we and where should we be heading. Mathematical Geology, 37(7):829-850.

Buccianti, A., Mateu-Figueras, G, and Pawlowsky-Glahn, V. (eds.), 2006. Compositional data analysis in the geosciences: from theory to practice. The Geological Society Publishing House, Bath, U.K. Special Publication 264, 224 p.

Janousek, V., Farrow, C.M. and Erban, V., 2006. Interpretation of whole-rock geochemical data in igneous geochemistry introducing Geochemical Data Toolkit (GCDkit). Journal of Petrology, 47(6):1255-1259.

Reimann, C., Filzmoser, P., Garrett, R. and Dutter, R., 2008. Statistical Data Analysis Explained: Applied Environmental Statistics with R. Wiley, 362 p.

See Also

clr, ilr, ltdl.fix.df, remove.na

Examples

# NOT RUN {
## Make test data available
data(sind)
sind.mat <- as.matrix(sind[, -c(1:3)])

## Undertake clr transform, note necessity
## of converting percent Fe to mg/kg
sind.mat[, 2] <- sind.mat[, 2] * 10000
temp <- clr(sind.mat)
temp

## Clean-up and detach test data
rm(sind.mat)
rm(temp)
# }