fitted.symcoca {cocorresp}R Documentation

Fitted values of a Symmetric Co-Correpsondence analysis model.

Description

Calculates and extracts the fitted values of a Symmetric Co-Correpsondence analysis model.

Usage

## S3 method for class 'symcoca'
fitted(object, which = c("y1","y2"), ...)

Arguments

object

an object of class "symcoca"

which

character; should the response or predictor scores be plotted. Can be specified in several ways: response choices are one from c("y", "Y", "y1", "response"); predictor choices are one from c("x", "X", "y2", "predictor").

...

arguments to be passed to other methods.

Value

A list with the following components:

Y

the fitted values for the “response” matrix.

X

the fitted values for the “predictor” matrix.

nam.dat

a vector containing the names of the “response” and “predictor” matrices respectively. Used for printing the results.

Note

This function needs an update and to allow option to restrict fitted values to specified axes, and the names of the returned objects need making more obvious!

Author(s)

Gavin L. Simpson, based on Matlab code by C.J.F. ter Braak and A.P. Schaffers.

References

Ter Braak, C.J.F and Schaffers, A.P. (2004) Co-Correspondence Analysis: a new ordination method to relate two community compositions. Ecology 85(3), 834–846

See Also

The model fitting function coca

Examples

## symmetric CoCA
data(beetles)
data(plants)

## log transform the bettle data
beetles <- log(beetles + 1)

## fit the model
bp.sym <- coca(beetles ~ ., data = plants, method = "symmetric")

## fitted values
bp.fit <- fitted(bp.sym)
bp.fit

## fitted values for beetles only
beetle.fit <- fitted(bp.sym, which = "y1")

[Package cocorresp version 0.4-3 Index]