varExpl: Variance explained by ordination axes

In gavinsimpson/analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Description

Extracts information about the variance explained by ordination axes and expresses it in a variety of ways.

Usage

varExpl(object, ...)

## S3 method for class 'cca'
varExpl(object, axes = 1L, cumulative = FALSE,
        pcent = FALSE, ...)

## S3 method for class 'prcurve'
varExpl(object, pcent = FALSE, ...)

Arguments

object	an R object of an appropriate type. Currently only for objects that inherit from classes "cca" or "prcurve".
axes	numeric vector indicating which axes to compute variance explained for.
cumulative	logical; should the variance be explained as a cumulative sum over the axes?
pcent	logical; should the variance explained be expressed as a percentage of the total variance.
...	additional arguments passed to other methods. Currently not used.

Value

A numeric vector variance explained by each axis.

Author(s)

Gavin L. Simpson

See Also

See cca and prcurve for functions that produce objects that varExpl() can work with.

Examples

data(abernethy)

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

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

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

gavinsimpson/analogue documentation built on June 17, 2021, 2:37 a.m.