scores.predcoca {cocorresp} | R Documentation |
Function to access either species or site scores for specified axes in co-correspondence analysis ordination methods.
## 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, ...)
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. |
Implements a scores
method for symmetric
co-correspondence analysis ordination results.
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. |
...
Gavin L. Simpson, based on Matlab code by C.J.F. ter Braak and A.P. Schaffers.
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
scores
, for further details on the method.
## 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)