scores.predcoca {cocorresp}R Documentation

Get Species or Site Scores from an Ordination

Description

Function to access either species or site scores for specified axes in co-correspondence analysis ordination methods.

Usage


## S3 method for class 'predcoca':
scores(x, choices = c(1, 2),
       display = c("site","species"), ...)

## S3 method for class 'symcoca':
scores(x, choices = c(1, 2),
       display = c("site","species"), scaling = 1, ...)

Arguments

x an ordination result
display partial match to access scores for “sites” or “species”.
choices the ordination axes to return.
scaling whether the species scores should be rescaled to the quarter root of the eigenvalues using rescale.symcoca.
... arguments to be passed to other methods.

Details

Implements a scores method for symmetric co-correspondence analysis ordination results.

Value

A list with two components containing matrices of the requested scores:

species A list with two components, U1 and U2, containing the species scores for the response matrix Y and the predictor matrix X respectively.
sites A list with two components, X1 and X2, containing the site scores for the response matrix Y and the predictor matrix X respectively.

...

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

scores, for further details on the method.

Examples

## load some data
data(beetles)
data(plants)
## log transform the bettle data
beetles <- log(beetles + 1)
## fit the model, a symmetric CoCA
bp.sym <- coca(beetles ~ ., data = plants, method = "symmetric")
## extract the scores
scores(bp.sym)

## predictive CoCA using SIMPLS and formula interface
bp.pred <- coca(beetles ~ ., data = plants)
scores(bp.pred)

[Package cocorresp version 0.1-7 Index]