Internal cocorresp Functions

Internal cocorresp functions.

predcoca.simpls, predcoca.eigen and symcoca perform the actual fitting of Co-CA models.

predcoca.eigen(y, x, R0 = NULL, n.axes = NULL, nam.dat = NULL)

predcoca.simpls(y, x, R0 = NULL, n.axes = NULL, nam.dat = NULL)

symcoca(y, x, n.axes = NULL, R0 = NULL,
        symmetric = FALSE, nam.dat = NULL)

Arguments

y	a data frame containing the response community data matrix.
x	a data frame containing the predictor community data matrix.
R0	a vector of length nrow(y) of user supplied weights for \(R_0\). If weights = NULL (default) then the weights are determined from y (default) or x and y (symmetric = TRUE only).
n.axes	the number of CoCA axes to extract. If missing (default) the n.axes is \(min(ncol(y), ncol(x), nrow(y), nrow(x)) - 1\).
symmetric	if method is "symmetric" then symmetric determines whether weights for \(R_0\) are symmetric and taken as the average of the row sums of x and y (symmetric = TRUE). If symmetric = FALSE (default) then the weights \(R_0\) are taken as the row sums of y unless user defined weights are provided via argument weights. Ignored if method is "predictive".
nam.dat	an optional list with elements namY and namX containing the names of y and x respectively. Used to label printed output. If missing the names of are deduced from y and x.
Y	a matrix for which standardised chi-square residuals are to be calculated.
eps	tolerance - leave as default.

Details

These are not to be called by the user.

predcoca.simpls, predcoca.eigen and symcoca perform the actual model fitting but are not meant to be called by the user as coca pre-processes the input data before calling these functions.