ade4 (version 1.7-5)

wca: Within-Class Analysis

Description

Performs a particular case of an Orthogonal Principal Component Analysis with respect to Instrumental Variables (orthopcaiv), in which there is only a single factor as covariable.

Usage

within(dudi, fac, scannf = TRUE, nf = 2)
"wca"(x, fac, scannf = TRUE, nf = 2, ...)

Arguments

dudi

a duality diagram, object of class dudi obtained from the functions dudi.coa, dudi.pca,...

x

a duality diagram, object of class dudi from one of the functions dudi.coa, dudi.pca,...

fac

a factor partitioning the rows of dudi$tab in classes

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

...

further arguments passed to or from other methods

Value

Returns a list of the sub-class within in the class dudi

References

Benzécri, J. P. (1983) Analyse de l'inertie intra-classe par l'analyse d'un tableau de correspondances. Les Cahiers de l'Analyse des données, 8, 351--358. 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.

Examples

data(meaudret)
pca1 <- dudi.pca(meaudret$env, scan = FALSE, nf = 4)
wit1 <- wca(pca1, meaudret$design$site, scan = FALSE, nf = 2)

if(adegraphicsLoaded()) {
  g1 <- s.traject(pca1$li, meaudret$design$site, psub.text = "Principal Component Analysis", 
    plines.lty = 1:nlevels(meaudret$design$site), psub.cex = 1.5, plot = FALSE)
  g2 <- s.traject(wit1$li, meaudret$design$site, 
    psub.text = "Within site Principal Component Analysis", 
    plines.lty = 1:nlevels(meaudret$design$site), psub.cex = 1.5, plot = FALSE)
  g3 <- s.corcircle (wit1$as, plot = FALSE)
  G <- ADEgS(list(g1, g2, g3), layout = c(2, 2))
  
} else {
  par(mfrow = c(2, 2))
  s.traject(pca1$li, meaudret$design$site, sub = "Principal Component Analysis", csub = 1.5)
  s.traject(wit1$li, meaudret$design$site, sub = "Within site Principal Component Analysis", 
    csub = 1.5)
  s.corcircle (wit1$as)
  par(mfrow = c(1,1))
}
plot(wit1)