# 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.