dudi.pco {ade4}R Documentation

Principal Coordinates Analysis

Description

dudi.pco performs a principal coordinates analysis of an Euclidean distance matrix and returns the results as objects of class pco and dudi.

Usage

dudi.pco(d, row.w = "uniform", scannf = TRUE, nf = 2, 
    full = FALSE, tol = 1e-07)
scatter.pco (x, xax = 1, yax = 2, clab.row = 1, posieig = "top", 
    sub = NULL, csub = 2, ...) 

Arguments

d an object of class 'dist' containing an Euclidean distance matrix.
row.w an optional distance matrix row weights. If not null, must be a vector of positive numbers with length equal to the size of the distance matrix
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
full a logical value indicating whether all the axes should be kept
tol a tolerance threshold to test whether the distance matrix is Euclidean : an eigenvalue is considered positive if it is larger than -tol*lambda1 where lambda1 is the largest eigenvalue.
x an object of class pco
xax the column number for the x-axis
yax the column number for the y-axis
clab.row a character size for the row labels
posieig if "top" the eigenvalues bar plot is upside, if "bottom" it is downside, if "none" no plot
sub a string of characters to be inserted as legend
csub a character size for the legend, used with par("cex")*csub
... further arguments passed to or from other methods

Value

dudi.pco returns a list of class 'pco' and 'dudi'. See dudi

References

Gower, J. C. (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53, 325–338.

Examples

data(yanomama)
gen <- quasieuclid(as.dist(yanomama$gen))
geo <- quasieuclid(as.dist(yanomama$geo))
ant <- quasieuclid(as.dist(yanomama$ant))
geo1 <- dudi.pco(geo, scann = FALSE, nf = 3)
gen1 <- dudi.pco(gen, scann = FALSE, nf = 3)
ant1 <- dudi.pco(ant, scann = FALSE, nf = 3)
plot(coinertia(ant1, gen1, scann = FALSE))

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