R: Between-class coinertia analysis

bca.coinertia {ade4} | R Documentation

## Between-class coinertia analysis

### Description

Performs a between-class analysis after a coinertia analysis

### Usage

    ## S3 method for class 'coinertia'
    bca(x, fac, scannf = TRUE, nf = 2, ...)

### Arguments

`x` | a coinertia analysis (object of class coinertia) obtained by the function coinertia
`fac` | a factor partitioning the rows in classes
`scannf` | a logical value indicating whether the eigenvalues barplot should be displayed
`nf` | if scannf FALSE, an integer indicating the number of kept axes
`...` | further arguments passed to or from other methods

### Details

This analysis is equivalent to do a between-class analysis on each initial dudi, and a coinertia analysis on the two between analyses. This function returns additional outputs for the interpretation.

### Value

An object of the class `betcoi`. Outputs are described by the `print` function

### Note

To avoid conflict names with the `base:::within` function, the function `within` is now deprecated and removed. To be consistent, the `betweencoinertia` function is also deprecated and is replaced by the method `bca.coinertia` of the new generic `bca` function.

### Author(s)

Stéphane Dray stephane.dray@univ-lyon1.fr and Jean Thioulouse jean.thioulouse@univ-lyon1.fr

### References

Franquet E., Doledec S., and Chessel D. (1995) Using multivariate analyses for separating spatial and temporal effects within species-environment relationships. Hydrobiologia, 300, 425–431.

### See Also

`coinertia`, `bca`

### Examples

    data(meaudret)
    pca1 <- dudi.pca(meaudret$env, scan = FALSE, nf = 4)
    pca2 <- dudi.pca(meaudret$spe, scal = FALSE, scan = FALSE, nf = 4)

    bet1 <- bca(pca1, meaudret$design$site, scan = FALSE, nf = 2)
    bet2 <- bca(pca2, meaudret$design$site, scan = FALSE, nf = 2)
    coib <- coinertia(bet1, bet2, scannf = FALSE)

    coi <- coinertia(pca1, pca2, scannf = FALSE, nf = 3)
    coi.b <- bca(coi,meaudret$design$site, scannf = FALSE)
    ## coib and coi.b are equivalent

    plot(coi.b)

[Package ade4 version 1.7-15 Index]