wca function

Within-Class Analysis

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.

## S3 method for class 'dudi'
wca(x, fac, scannf = TRUE, nf = 2, ...)

Arguments

• 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

Returns

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

• tab: a data frame containing the transformed data (substraction of the class mean)

• call: the matching call

• nf: number of kept axes

• rank: the rank of the analysis

• ratio: percentage of within-class inertia

• eig: a numeric vector containing the eigenvalues

• lw: a numeric vector of row weigths

• cw: a numeric vector of column weigths

• tabw: a numeric vector of class weigths

• fac: the factor defining the classes

• li: data frame row coordinates

• l1: data frame row normed scores

• co: data frame column coordinates

• c1: data frame column normed scores

• ls: data frame supplementary row coordinates

• as: data frame inertia axis onto within axis

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.

Note

To avoid conflict names with the base:::within function, the function within is now deprecated and removed. It is replaced by the method wca.dudi of the new generic wca function.

Author(s)

Daniel Chessel

Anne-Béatrice Dufour anne-beatrice.dufour@univ-lyon1.fr

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)