gradientDist: Positions of samples along a unit-length ordination gradient.

Description

Extracts information as to the locations of samples along an ordination gradient. gradientDist() standardises the entire gradient to the interval 0, ..., 1, to allow comparison between methods or data sets.

Usage

gradientDist(object, ...)
# S3 method for default
gradientDist(object, na.rm = TRUE, ...)
# S3 method for cca
gradientDist(object, na.rm = TRUE, axis = 1L,
             scaling = 0, ...)
# S3 method for prcurve
gradientDist(object, na.rm = TRUE, ...)

Value

A numeric vector of positions along the gradient, scaled to the range 0, ..., 1.

Arguments

object: an R object of an appropriate type. For the default method, any R object that can be coerced to a vector.
na.rm: logical; should missing values be removed?
axis: numeric, length 1; the ordination axis to take as the gradient.
scaling: Scaling to apply to the site scores. Default is to do no scaling. See scores.cca for details.
...: additional arguments passed to other methods. In the "cca" method, these are also passed to scores.cca.

Author

Gavin L. Simpson

Examples

Run this code


data(abernethy)

## Remove the Depth and Age variables
abernethy2 <- abernethy[, -(37:38)]

## Fit PCA
aber.pca <- rda(abernethy2)

## Distance along the first PCA axis
gradientDist(aber.pca)