Between-class coinertia analysis

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

Value

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

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.

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.

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

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

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)
#> Error in s.arrow(dfxy = coi.b$aX, xax = 1, yax = 2, plot = FALSE, storeData = TRUE,     pos = -3, psub = list(text = "Unconstrained axes (X)"), plabels = list(        cex = 1.25)): non convenient selection for dfxy (can not be converted to dataframe)