between {ade4}

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 [e-mail]
Stéphane Dray [e-mail]

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)