coinertia {ade4} | R Documentation

## Coinertia Analysis

### Description

The coinertia analysis performs a double inertia analysis of two arrays.

### Usage

    coinertia(dudiX, dudiY, scannf = TRUE, nf = 2)
    plot.coinertia (x, xax = 1, yax = 2, ...)
    print.coinertia (x, ...)
    summary.coinertia (object, ...)

### Arguments

`dudiX` | a duality diagram providing from one of the functions dudi.coa, dudi.pca, ...
`dudiY` | a duality diagram providing from one of the functions dudi.coa, dudi.pca, ...
`scannf` | a logical value indicating whether the eigenvalues bar plot should be displayed
`nf` | if scannf FALSE, an integer indicating the number of kept axes
`x, object` | an object of class 'coinertia'
`xax, yax` | the numbers of the x-axis and the y-axis
`...` | further arguments passed to or from other methods

### Value

Returns a list of class 'coinertia', sub-class 'dudi' containing:

`call` | call
`rank` | rank
`nf` | a numeric value indicating the number of kept axes
`RV` | a numeric value, the RV coefficient
`eig` | a numeric vector with all the eigenvalues
`lw` | a numeric vector with the rows weigths (crossed array)
`cw` | a numeric vector with the columns weigths (crossed array)
`tab` | a crossed array (CA)
`li` | Y col = CA row: coordinates
`l1` | Y col = CA row: normed scores
`co` | X col = CA column: coordinates
`c1` | X col = CA column: normed scores
`lX` | the row coordinates (X)
`mX` | the normed row scores (X)
`lY` | the row coordinates (Y)
`mY` | the normed row scores (Y)
`aX` | the axis onto co-inertia axis (X)
`aY` | the axis onto co-inertia axis (Y)

### WARNING

IMPORTANT : `dudi1` and `dudi2` must have identical row weights.

### Author(s)

Daniel Chessel chessel@biomserv.univ-lyon1.fr

### References

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

### Examples

    data(doubs)
    dudi1 <- dudi.pca(doubs$mil, scale = TRUE, scan = FALSE, nf = 3)
    dudi2 <- dudi.pca(doubs$poi, scale = FALSE, scan = FALSE, nf = 2)
    coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
    s.arrow(coin1$l1, clab = 0.7)

    s.arrow(coin1$c1, clab = 0.7)

    par(mfrow = c(1,2))
    s.corcircle(coin1$aX)
    s.corcircle(coin1$aY)
    par(mfrow = c(1,1))

    coin1
    summary(coin1)
    plot(coin1)

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