decostand {vegan}R Documentation

Standardizaton Methods for Community Ecology

Description

The function provides some popular (and effective) standardization methods for community ecologists.

Usage

decostand(x, method, MARGIN)
wisconsin(x)

Arguments

x Community data matrix.
method Standardization method.
MARGIN Margin, if default is not acceptable.

Details

The function offers following standardization methods for community data:

Standardization, as contrasted to transformation, means that the entries are transformed relative to other entries.

All methods have a default margin. MARGIN=1 means rows (sites in a normal data set) and MARGIN=2 means columns (species in a normal data set).

Command wisconsin is a shortcut to common Wisconsin double standardization where species (MARGIN=2) are first standardized by maxima (max) and then sites (MARGIN=1) by site totals (tot).

Value

Returns the standardized data frame.

Note

Common transformations can be made with standard R functions.

Author(s)

Jari Oksanen

References

Legendre, P. & Gallagher, E.D. (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271–280.

Oksanen, J. (1983) Ordination of boreal heath-like vegetation with principal component analysis, correspondence analysis and multidimensional scaling. Vegetatio 52, 181–189.

Examples

data(varespec)
sptrans <- decostand(varespec, "max")
apply(sptrans, 2, max)
sptrans <- wisconsin(varespec)
# Chi-square: Similar but not identical to Correspondence Analysis.
sptrans <- decostand(varespec, "chi.square")
plot(procrustes(rda(sptrans), cca(varespec)))
# Hellinger transformation (Legendre & Callagher 2001):
sptrans <- sqrt(decostand(varespec, "total"))

[Package vegan version 1.6-8 Index]