Last data update: 2014.03.03
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R: Coinertia Analysis
Coinertia Analysis
Description
The coinertia analysis performs a double inertia analysis of two tables.
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, ...
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dudiY |
a duality diagram providing from one of the functions dudi.coa, dudi.pca, ...
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scannf |
a logical value indicating whether the eigenvalues bar plot should be displayed
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nf |
if scannf FALSE, an integer indicating the number of kept axes
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x, object |
an object of class 'coinertia'
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xax, yax |
the numbers of the x-axis and the y-axis
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... |
further arguments passed to or from other methods
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Value
Returns a list of class 'coinertia', sub-class 'dudi' containing:
call |
call
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rank |
rank
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nf |
a numeric value indicating the number of kept axes
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RV |
a numeric value, the RV coefficient
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eig |
a numeric vector with all the eigenvalues
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lw |
a numeric vector with the rows weigths (crossed table)
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cw |
a numeric vector with the columns weigths (crossed table)
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tab |
a crossed table (CT)
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li |
CT row scores (cols of dudiY)
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l1 |
Principal components (loadings for cols of dudiY)
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co |
CT col scores (cols of dudiX)
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c1 |
Principal axes (cols of dudiX)
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lX |
Row scores (rows of dudiX)
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mX |
Normed row scores (rows of dudiX)
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lY |
Row scores (rows of dudiY)
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mY |
Normed row scores (rows of dudiY)
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aX |
Correlations between dudiX axes and coinertia axes
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aY |
Correlations between dudiY axes and coinertia axes
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WARNING
IMPORTANT : dudi1 and dudi2 must have identical row weights.
Author(s)
Daniel Chessel
Anne B Dufour anne-beatrice.dufour@univ-lyon1.fr
References
Dolédec, 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$env, scale = TRUE, scan = FALSE, nf = 3)
dudi2 <- dudi.pca(doubs$fish, scale = FALSE, scan = FALSE, nf = 2)
coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
coin1
summary(coin1)
if(adegraphicsLoaded()) {
g1 <- s.arrow(coin1$l1, plab.cex = 0.7)
g2 <- s.arrow(coin1$c1, plab.cex = 0.7)
g3 <- s.corcircle(coin1$aX, plot = FALSE)
g4 <- s.corcircle(coin1$aY, plot = FALSE)
cbindADEg(g3, g4, plot = TRUE)
g5 <- plot(coin1)
} else {
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))
plot(coin1)
}
Results
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