bca {ade4}R Documentation

Between-Class Analysis

Description

Performs a particular case of a Principal Component Analysis with respect to Instrumental Variables (pcaiv), in which there is only a single factor as explanatory variable.

Usage

between(dudi, fac, scannf = TRUE, nf = 2)
## S3 method for class 'dudi'
bca(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 barplot should be displayed

nf

if scannf FALSE, a numeric value indicating the number of kept axes

...

further arguments passed to or from other methods

Value

Returns a list of class dudi, subclass 'between' containing

tab

a data frame class-variables containing the means per class for each variable

cw

a numeric vector of the column weigths

lw

a numeric vector of the class weigths

eig

a numeric vector with all the eigenvalues

rank

the rank of the analysis

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 matching call

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

Note

To avoid conflict names with the base:::within function, the function within is now deprecated and will be removed. To be consistent, the between function is also deprecated and is replaced by the method bca.dudi of the new generic bca function.

Author(s)

Daniel Chessel
Anne B Dufour anne-beatrice.dufour@univ-lyon1.fr

References

Dol├ędec, 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$env, scan = FALSE, nf = 4)
pca2 <- dudi.pca(meaudret$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$site, psub.text = "Principal Component Analysis (env)",
    plot = F)
  g2 <- s.class(pca2$li, meaudret$design$site, psub.text = "Principal Component Analysis (spe)",
    plot = F)
  g3 <- s.class(bet1$ls, meaudret$design$site, psub.text = "Between sites PCA (env)", plot = F)
  g4 <- s.class(bet2$ls, meaudret$design$site, psub.text = "Between sites PCA (spe)", plot = F)
  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 1.7-4 Index]