# coinertia: Coinertia Analysis In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

## Description

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

## Usage

 1 2 3 4 5 6 7 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 table) cw a numeric vector with the columns weigths (crossed table) tab a crossed table (CT) li CT row scores (cols of dudiY) l1 Principal components (loadings for cols of dudiY) co CT col scores (cols of dudiX) c1 Principal axes (cols of dudiX) lX Row scores (rows of dudiX) mX Normed row scores (rows of dudiX) lY Row scores (rows of dudiY) mY Normed row scores (rows of dudiY) aX Correlations between dudiX axes and coinertia axes aY Correlations between dudiY axes and coinertia axes

## WARNING

IMPORTANT : dudi1 and dudi2 must have identical row weights.

## Author(s)

Daniel Chessel
Anne-Béatrice Dufour [email protected]

## 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

 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 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) }

ade4 documentation built on Aug. 31, 2018, 5:04 p.m.