vegan (version 1.0-1)

decostand: Standardizaton Methods for Community Ecology

Description

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

Usage

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

Arguments

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

Value

  • Returns the standardized matrix.

Details

The function offers following standardization methods for community data:
  • total: divide by margin total (default margin 1).
  • max: divide by margin maximum (default margin 2).
  • freq: divide by margin maximum and multiply by number of non-zero items, so that the average of non-zero entries is one (default margin 2).
  • normalize: make margin sum of squares equal to unity (default margin 1).
  • range: standardize values into range 0...1 (default margin 2).
  • standardize: scale into zero mean and unit variance (default margin 2).
  • pa: scale into presence/absence scale (0/1).
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).

Examples

Run this code
data(varespec)
sptrans <- decostand(varespec, "max")
apply(sptrans, 1, max)
sptrans <- wisconsin(varespec)

Run the code above in your browser using DataCamp Workspace