fitCoinertia: Co-inertia analysis

Description

Performs a co-inertia of the triplets \((Q_1,K_1,R_0)\) and \((Q_2,K_2,R_0)\).

Usage

fitCoinertia(X, Dp, Y, Dq, Dn, n.axes)

# S3 method for fitCoinertia
summary(object, ...)

Value

A list with the following components:

U1: column weights of X.
U2: column weights of Y.
X1: rowscores of X.
X2: rowscores of Y.
lambda: the Eigenvalues (squares of the singular values).
n.axes: number of axes requested.
call: the matched function call.

Arguments

X: \(Q_1\), matrix of expected abundances under row-column independence in the original Y species matrix when treated as a contingency table.
Dp: \(K_1\), species (column) weights for X.
Y: \(Q_2\), matrix of expected abundances under row-column independence in the original X species matrix when treated as a contingency table.
Dq: \(K_2\), species (column) weights for Y.
Dn: site weights \(R_0\).
n.axes: number of axes to calculate the co-inertia analysis for.
object: an object of class coinertia.
axes: the number of axes to display when printing.

...: arguments passed to other functions. Currently ignored.

Author

Original Matlab code by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson.

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