between {ade4} | R Documentation

## Between-Class Analysis

### Description

Performs a particular case of a Principal Component Analysis with respect to Instrumental Variables, in which there is only one instrumental variable, and it is a factor.

### Usage

    between(dudi, fac, scannf = TRUE, nf = 2)
    plot.between(x, xax = 1, yax = 2, ...)
    print.between(x, ...)

### Arguments

`dudi` | a duality diagram, object of class `dudi` from one of the functions dudi.coa, dudi.pca, ...
`fac` | a factor partitioning the rows of `dudi$tab` in classes
`scannf` | a logical value indicating whether the eigenvalues bar plot should be displayed
`nf` | if scannf FALSE, a numeric value indicating the number of kept axes
`x` | an object of class 'between'
`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 subclass 'between' of class 'dudi' (see `dudi`)

`tab` | a data frame class-variables, array of variables means in each class
`cw` | a numeric vector of the column weigths
`lw` | a numeric vector of the group weigths
`eig` | a numeric vector with all the eigenvalues
`rank` | an integer
`nf` | an integer value indicating the number of kept axes
`c1` | a data frame with the column normed scores
`l1` | a data frame with the class normed scores
`co` | a data frame with the column coordinates
`li` | a data frame with the class coordinates
`call` | the origin
`ratio` | the bewteen-class inertia percentage
`ls` | a data frame with the row coordinates
`as` | a data frame containing the projection of inertia axes onto between axes

### Author(s)

Daniel Chessel chessel@biomserv.univ-lyon1.fr

### References

Dolédec, S. and Chessel, D. (1987) Rythmes saisonniers et composantes stationnelles en milieu aquatique I- Description d'un plan d'observations complet par projection de variables. Acta Oecologica, Oecologia Generalis, 8, 3, 403–426.

### Examples

    data(meaudret)
    par(mfrow = c(2,2))
    pca1 <- dudi.pca(meaudret$mil, scan = FALSE, nf = 4)
    s.class(pca1$li, meaudret$plan$sta,
        sub = "Principal Component Analysis (mil)", csub = 1.75)
    pca2 <- dudi.pca(meaudret$fau, scal = FALSE, scan = FALSE, nf = 4)
    s.class(pca2$li, meaudret$pla$sta,
        sub = "Principal Component Analysis (fau)", csub = 1.75)
    bet1 <- between(pca1, meaudret$plan$sta, scan = FALSE, nf = 2)
    bet2 <- between(pca2, meaudret$plan$sta, scan = FALSE, nf = 2)
    s.class(bet1$ls, meaudret$plan$sta,
        sub = "Between sites PCA (mil)", csub = 1.75)
    s.class(bet2$ls, meaudret$plan$sta,
        sub = "Between sites PCA (fau)", csub = 1.75)

    par(mfrow = c(1,1))
    coib <- coinertia(bet1, bet2, scann = FALSE)
    plot(coib)

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