between {ade4}R Documentation

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)
## S3 method for class 'between':
plot(x, xax = 1, yax = 2, ...) 
## S3 method for class 'between':
print(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

Author(s)

Daniel Chessel
Anne B Dufour dufour@biomserv.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)
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)

Worked out examples


> library(ade4)
> ### Name: between
> ### Title: Between-Class Analysis
> ### Aliases: between print.between plot.between
> ### Keywords: multivariate
> 
> ### ** 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)
> 
> 
> 
> 

[Package ade4 Index]