ade4: dudi.pco – R documentation

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dudi.pco

Principal Coordinates Analysis

Description

dudi.pco performs a principal coordinates analysis of a 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)
## S3 method for class 'pco'
scatter(x, xax = 1, yax = 2, clab.row = 1, posieig = "top", 
    sub = NULL, csub = 2, ...)

Arguments

`d`	an object of class `dist` containing a 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

Author(s)

Daniel Chessel
Anne-Béatrice Dufour anne-beatrice.dufour@univ-lyon1.fr

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))

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release