fitted.symcoca function

Fitted values of a Symmetric Co-Correpsondence analysis model.

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

## 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.

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!

Returns

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.

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")