within {ade4}R Documentation

Within Analyses

Description

performs within analyses on an object of class dudi.

Usage

within(dudi, fac, scannf = TRUE, nf = 2) 
## S3 method for class 'within':
plot(x, xax = 1, yax = 2, ...) 
## S3 method for class 'within':
print(x, ...)

Arguments

dudi an object of class dudi
fac a factor distributing 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
xax the column number for the x-axis
yax the column number for the y-axis
x an object of class 'within'
... further arguments passed to or from other methods

Value

Returns a list of the sub-class within in the class dudi
call origine
nf number of axis saved
rank rank
ratio percentage of within inertia
eig numeric eigen values
lw numeric row weigths
cw numeric col weigths
tabw numeric table weigths
fac factor for grouping
tab data frame class-variables
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

Author(s)

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

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)
par(mfrow = c(2,2))
pca1 <- dudi.pca(meaudret$mil, scan = FALSE, nf = 4)
s.traject(pca1$li, meaudret$plan$sta, 
    sub = "Principal Component Analysis", csub = 1.5)
wit1 <- within(pca1, meaudret$plan$sta, scan = FALSE, nf = 2)
s.traject(wit1$li, meaudret$plan$sta, 
    sub = "Within site Principal Component Analysis", csub = 1.5)
s.corcircle (wit1$as)
par(mfrow = c(1,1))
plot(wit1)

Worked out examples


> library(ade4)
> ### Name: within
> ### Title: Within Analyses
> ### Aliases: within print.within plot.within
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(meaudret)
> par(mfrow = c(2,2))
> pca1 <- dudi.pca(meaudret$mil, scan = FALSE, nf = 4)
> s.traject(pca1$li, meaudret$plan$sta, 
+     sub = "Principal Component Analysis", csub = 1.5)
> wit1 <- within(pca1, meaudret$plan$sta, scan = FALSE, nf = 2)
> s.traject(wit1$li, meaudret$plan$sta, 
+     sub = "Within site Principal Component Analysis", csub = 1.5)
> s.corcircle (wit1$as)
> par(mfrow = c(1,1))
> plot(wit1)
> 
> 
> 
> 

[Package ade4 Index]