coinertia {ade4}R Documentation

Coinertia Analysis

Description

The coinertia analysis performs a double inertia analysis of two arrays.

Usage

coinertia(dudiX, dudiY, scannf = TRUE, nf = 2)
## S3 method for class 'coinertia':
plot (x, xax = 1, yax = 2, ...) 
## S3 method for class 'coinertia':
print (x, ...) 
## S3 method for class 'coinertia':
summary (object, ...) 

Arguments


dudiX a duality diagram providing from one of the functions dudi.coa, dudi.pca, ...
dudiY a duality diagram providing from one of the functions dudi.coa, dudi.pca, ...
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
x, object an object of class 'coinertia'
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 class 'coinertia', sub-class 'dudi' containing:
call call
rank rank
nf a numeric value indicating the number of kept axes
RV a numeric value, the RV coefficient
eig a numeric vector with all the eigenvalues
lw a numeric vector with the rows weigths (crossed array)
cw a numeric vector with the columns weigths (crossed array)
tab a crossed array (CA)
li Y col = CA row: coordinates
l1 Y col = CA row: normed scores
co X col = CA column: coordinates
c1 X col = CA column: normed scores
lX the row coordinates (X)
mX the normed row scores (X)
lY the row coordinates (Y)
mY the normed row scores (Y)
aX the axis onto co-inertia axis (X)
aY the axis onto co-inertia axis (Y)

WARNING

IMPORTANT : dudi1 and dudi2 must have identical row weights.

Author(s)

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

References

Dol├ędec, S. and Chessel, D. (1994) Co-inertia analysis: an alternative method for studying species-environment relationships. Freshwater Biology, 31, 277–294.

Dray, S., Chessel, D. and J. Thioulouse (2003) Co-inertia analysis and the linking of the ecological data tables. Ecology, 84, 11, 3078–3089.

Examples

data(doubs)
dudi1 <- dudi.pca(doubs$mil, scale = TRUE, scan = FALSE, nf = 3)
dudi2 <- dudi.pca(doubs$poi, scale = FALSE, scan = FALSE, nf = 2)
coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
s.arrow(coin1$l1, clab = 0.7)

s.arrow(coin1$c1, clab = 0.7)

par(mfrow = c(1,2))
s.corcircle(coin1$aX)
s.corcircle(coin1$aY)
par(mfrow = c(1,1))
 
coin1
summary(coin1)
plot(coin1)

Worked out examples


> library(ade4)
> ### Name: coinertia
> ### Title: Coinertia Analysis
> ### Aliases: coinertia print.coinertia plot.coinertia summary.coinertia
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(doubs)
> dudi1 <- dudi.pca(doubs$mil, scale = TRUE, scan = FALSE, nf = 3)
> dudi2 <- dudi.pca(doubs$poi, scale = FALSE, scan = FALSE, nf = 2)
> coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
> s.arrow(coin1$l1, clab = 0.7)
> 
> s.arrow(coin1$c1, clab = 0.7)
> 
> par(mfrow = c(1,2))
> s.corcircle(coin1$aX)
> s.corcircle(coin1$aY)
> par(mfrow = c(1,1))
> 
> coin1
Coinertia analysis
call: coinertia(dudiX = dudi1, dudiY = dudi2, scannf = FALSE, nf = 2)
class: coinertia dudi 

$rank (rank)     : 11
$nf (axis saved) : 2
$RV (RV coeff)   : 0.4505569

eigen values: 119 13.87 0.7566 0.5278 0.2709 ...

  vector length mode    content                    
1 $eig   11     numeric eigen values               
2 $lw    27     numeric row weigths (crossed array)
3 $cw    11     numeric col weigths (crossed array)

   data.frame nrow ncol content                         
1  $tab       27   11   crossed array (CA)              
2  $li        27   2    Y col = CA row: coordinates     
3  $l1        27   2    Y col = CA row: normed scores   
4  $co        11   2    X col = CA column: coordinates  
5  $c1        11   2    X col = CA column: normed scores
6  $lX        30   2    row coordinates (X)             
7  $mX        30   2    normed row scores (X)           
8  $lY        30   2    row coordinates (Y)             
9  $mY        30   2    normed row scores (Y)           
10 $aX        3    2    axis onto co-inertia axis (X)   
11 $aY        2    2    axis onto co-inertia axis (Y)   

> summary(coin1)

Eigenvalues decomposition:
        eig     covar      sdX      sdY      corr
1 119.01942 10.909602 2.326324 6.422570 0.7301798
2  13.87137  3.724429 1.685078 2.863743 0.7718017

Inertia & coinertia X:
    inertia      max     ratio
1  5.411785 6.321624 0.8560752
12 8.251272 8.553220 0.9646978

Inertia & coinertia Y:
    inertia      max     ratio
1  41.24940 42.74627 0.9649824
12 49.45042 50.90461 0.9714331

RV:
 0.4505569 
> plot(coin1)
> 
> 
> 
> 

[Package ade4 Index]