R: Coinertia Analysis

coinertia {ade4} | R Documentation

## Coinertia Analysis

### Description

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

### Usage

    coinertia(dudiX, dudiY, scannf = TRUE, nf = 2)
    ## S3 method for class 'coinertia'
     plot(x, xax = 1, yax = 2, ...)
    ## S3 method for class 'coinertia'
     print(x, ...)
    ## S3 method for class 'coinertia'
     summary(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 table)
`cw` | a numeric vector with the columns weigths (crossed table)
`tab` | a crossed table (CT)
`li` | CT row scores (cols of dudiY)
`l1` | Principal components (loadings for cols of dudiY)
`co` | CT col scores (cols of dudiX)
`c1` | Principal axes (cols of dudiX)
`lX` | Row scores (rows of dudiX)
`mX` | Normed row scores (rows of dudiX)
`lY` | Row scores (rows of dudiY)
`mY` | Normed row scores (rows of dudiY)
`aX` | Correlations between dudiX axes and coinertia axes
`aY` | Correlations between dudiY axes and coinertia axes

### WARNING

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

### Author(s)

Daniel Chessel
Anne-Béatrice Dufour anne-beatrice.dufour@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.

Dray, S., Chessel, D. and J. Thioulouse (2003) Co-inertia analysis and the linking of the ecological data tables. Ecology, 84, 11, 3078–3089.

### Examples

    data(doubs)
    dudi1 <- dudi.pca(doubs$env, scale = TRUE, scan = FALSE, nf = 3)
    dudi2 <- dudi.pca(doubs$fish, scale = FALSE, scan = FALSE, nf = 2)
    coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
    coin1
    summary(coin1)

    if(adegraphicsLoaded()) {
      g1 <- s.arrow(coin1$l1, plab.cex = 0.7)
      g2 <- s.arrow(coin1$c1, plab.cex = 0.7)
      g3 <- s.corcircle(coin1$aX, plot = FALSE)
      g4 <- s.corcircle(coin1$aY, plot = FALSE)
      cbindADEg(g3, g4, plot = TRUE)
      g5 <- plot(coin1)

    } else {
    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))
    plot(coin1)
    }

[Package ade4 version 1.7-8 Index]