ade4 (version 1.2-2)

between: Between-Class Analysis

Description

Performs a particular case of a Principal Component Analysis with respect to Instrumental Variables, in which there is only one instrumental variable, and it is a factor.

Usage

between(dudi, fac, scannf = TRUE, nf = 2)
plot.between(x, xax = 1, yax = 2, ...) 
print.between(x, ...)

Arguments

dudi

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, a numeric value indicating the number of kept axes

x

an object of class 'between'

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 subclass 'between' of class 'dudi' (see dudi)
• tab
  a data frame class-variables, array of variables means in each class
• cw
  a numeric vector of the column weigths
• lw
  a numeric vector of the group weigths
• eig
  a numeric vector with all the eigenvalues
• rank
  an integer
• nf
  an integer value indicating the number of kept axes
• c1
  a data frame with the column normed scores
• l1
  a data frame with the class normed scores
• co
  a data frame with the column coordinates
• li
  a data frame with the class coordinates
• call
  the origin
• ratio
  the bewteen-class inertia percentage
• ls
  a data frame with the row coordinates
• as
  a data frame containing the projection of inertia axes onto between axes

References

Dol�dec, 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)
par(mfrow = c(2,2))
pca1 <- dudi.pca(meaudret$mil, scan = FALSE, nf = 4)
s.class(pca1$li, meaudret$plan$sta,
    sub = "Principal Component Analysis (mil)", csub = 1.75)
pca2 <- dudi.pca(meaudret$fau, scal = FALSE, scan = FALSE, nf = 4)
s.class(pca2$li, meaudret$pla$sta,
    sub = "Principal Component Analysis (fau)", csub = 1.75)
bet1 <- between(pca1, meaudret$plan$sta, scan = FALSE, nf = 2)
bet2 <- between(pca2, meaudret$plan$sta, scan = FALSE, nf = 2)
s.class(bet1$ls, meaudret$plan$sta,
    sub = "Between sites PCA (mil)", csub = 1.75)
s.class(bet2$ls, meaudret$plan$sta,
    sub = "Between sites PCA (fau)", csub = 1.75)

par(mfrow = c(1,1))
coib <- coinertia(bet1, bet2, scann = FALSE)
plot(coib)