coinertia {cocorresp} R Documentation

## 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

```coinertia(y, ...)

## Default S3 method:
coinertia(y, x, n.axes = NULL, weights = NULL,
symmetric = FALSE, ...)
```

### Arguments

 `y, x` matrices or data frames of the two data sets for which axes of covariance are sought. `n.axes` numeric; the number of coinertia axes to retain. `weights` a vector of weights for the samples. If `NULL`, weights are chosen from the row sums of `y` (```symmetric = FALSE```) or the average of the row sums of `y` and `x` (`symmetric = TRUE`). `symmetric` logical; should a symmetric set of weights be used. See Details. `...` arguments passed to other functions. Currently ignored.

### Value

An object of class `"coinertia"`, which is a list with the following components:

 `scores` a list of ordination scores, with components `species` and `sites`, each of which is a list with components `Y` and `X` that refer to the scores for the input matrices `y` and `x` respectively. `weights` numeric vector of row weights used in the analysis. `lambda` numeric vector of Eigenvalues. `n.axes` numeric; the number of coinertia axes extracted `symmetric` logical; was a symmetric analysis performed? `call` the matched call.

### Author(s)

Gavin L. Simpson, based on original Matlab code by C.J.F. ter Braak and A.P. Schaffers.

### 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

Doledec, S and Chessel, D. (1994) Co-inertia analysis: a method for studying species-environment relationships. Freshwater Biology 31, 277–294

`symcoca` for the function that calls `fitCoinertia` and `coinertiaI` for co-inertia analysis using identity matrices for K_1, K_2, and R_0.
```