Internal cocorresp Functions

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Description

Internal cocorresp functions.

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

Usage

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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.