R: Between-Class Analysis

between {ade4} | R Documentation

## Between-Class Analysis

### Description

Outputs and graphical representations of the results of a between-class analysis.

### Usage

    ## S3 method for class 'between'
    plot(x, xax = 1, yax = 2, ...)
    ## S3 method for class 'between'
    print(x, ...)
    ## S3 method for class 'betcoi'
    plot(x, xax = 1, yax = 2, ...)
    ## S3 method for class 'betcoi'
    print(x, ...)
    ## S3 method for class 'between'
    summary(object, ...)

### Arguments

`x,object` | an object of class `between` or `betcoi`
`xax, yax` | the column index of the x-axis and the y-axis
`...` | further arguments passed to or from other methods

### Author(s)

Daniel Chessel
Anne-Béatrice Dufour anne-beatrice.dufour@univ-lyon1.fr
Stéphane Dray stephane.dray@univ-lyon1.fr

### References

Dolédec, S. and Chessel, D. (1987) Rythmes saisonniers et composantes stationnelles en milieu aquatique I- Description d'un plan d'observations complet par projection de variables. Acta Oecologica, Oecologia Generalis, 8, 3, 403–426.

### See Also

`bca.dudi`, `bca.coinertia`

### Examples

    data(meaudret)

    pca1 <- dudi.pca(meaudret$env, scan = FALSE, nf = 4)
    pca2 <- dudi.pca(meaudret$spe, scal = FALSE, scan = FALSE, nf = 4)
    bet1 <- bca(pca1, meaudret$design$site, scan = FALSE, nf = 2)
    bet2 <- bca(pca2, meaudret$design$site, scan = FALSE, nf = 2)

    if(adegraphicsLoaded()) {
      g1 <- s.class(pca1$li, meaudret$design$site, psub.text = "Principal Component Analysis (env)",
        plot = FALSE)
      g2 <- s.class(pca2$li, meaudret$design$site, psub.text = "Principal Component Analysis (spe)",
        plot = FALSE)
      g3 <- s.class(bet1$ls, meaudret$design$site, psub.text = "Between sites PCA (env)",
        plot = FALSE)
      g4 <- s.class(bet2$ls, meaudret$design$site, psub.text = "Between sites PCA (spe)",
        plot = FALSE)
      G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))

    } else {
      par(mfrow = c(2, 2))
      s.class(pca1$li, meaudret$design$site, sub = "Principal Component Analysis (env)", csub = 1.75)
      s.class(pca2$li, meaudret$design$site, sub = "Principal Component Analysis (spe)", csub = 1.75)
      s.class(bet1$ls, meaudret$design$site, sub = "Between sites PCA (env)", csub = 1.75)
      s.class(bet2$ls, meaudret$design$site, sub = "Between sites PCA (spe)", csub = 1.75)
      par(mfrow = c(1,1))
    }

    coib <- coinertia(bet1, bet2, scann = FALSE)
    plot(coib)

[Package ade4 version 1.7-17 Index]