Get Species or Site Scores from an Ordination
Description
Function to access either species or site scores for specified axes in cocorrespondence analysis ordination methods.
Usage
1 2 3 4 5 6 7 
Arguments
x 
an ordination result 
display 
partial match to access scores for “sites”
“species”, “loadings” or “xmatrix”. The latter
two are only available for 
choices 
numeric; the ordination axes to return. 
scaling 
numeric; whether the species scores should be rescaled
to the quarter root of the eigenvalues using

... 
arguments to be passed to other methods. 
Details
Implements a scores
method for symmetric
cocorrespondence analysis ordination results.
Value
A list with one or more components containing matrices of the requested scores:
species 
A list with two components, 
sites 
A list with two components, 
loadings 
A list with two components, 
xmatrix 
The X matrix. For 
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) CoCorrespondence 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  ## 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
scr < scores(bp.sym)
## predictive CoCA using SIMPLS and formula interface
bp.pred < coca(beetles ~ ., data = plants)
scr2 < scores(bp.pred)
