# dudi.pco: Principal Coordinates Analysis In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

## 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

 ```1 2 3 4 5``` ```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

 ```1 2 3 4 5 6 7 8``` ```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)) ```

### Example output ```
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ade4 documentation built on June 17, 2021, 5:14 p.m.