dpcoa {ade4} | R Documentation

## Double principal coordinate analysis

### Description

Performs a double principal coordinate analysis

### Usage

    dpcoa (df, dis = NULL, scannf = TRUE, nf = 2, full = FALSE, tol = 1e-07)
    plot.dpcoa (x, xax = 1, yax = 2, option = 1:4, csize = 2, ...)
    print.dpcoa (x, ...)

### Arguments

`df` | a data frame with elements as rows, samples as columns and abundance or presence-absence as entries
`dis` | an object of class `dist` containing the distances between the elements.
`scannf` | a logical value indicating whether the eigenvalues bar plot should be displayed
`nf` | if scannf is FALSE, an integer indicating the number of kept axes
`full` | a logical value indicating whether all non null eigenvalues should be kept
`tol` | a tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
`x` | an object of class `dpcoa`
`xax` | the column number for the x-axis
`yax` | the column number for the y-axis
`option` | the function `plot.dpcoa` produces four graphs, `option` allows us to choose only some of them
`csize` | a size coefficient for symbols
`...` | `...` further arguments passed to or from other methods

### Value

Returns a list of class `dpcoa` containing:

`call` | call
`nf` | a numeric value indicating the number of kept axes
`w1` | a numeric vector containing the weights of the elements
`w2` | a numeric vector containing the weights of the samples
`eig` | a numeric vector with all the eigenvalues
`RaoDiv` | a numeric vector containing diversities within samples
`RaoDis` | an object of class `dist` containing the dissimilarities between samples
`RaoDecodiv` | a data frame with the decomposition of the diversity
`l1` | a data frame with the coordinates of the elements
`l2` | a data frame with the coordinates of the samples
`c1` | a data frame with the scores of the principal axes of the elements

### Author(s)

Daniel Chessel chessel@biomserv.univ-lyon1.fr
Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr
Anne B Dufour dufour@biomserv.univ-lyon1.fr

### References

Pavoine, S., Dufour, A.B. and Chessel, D. (in press) From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. Journal of Theoretical Biology.

### Examples

    data(humDNAm)
    dpcoahum <- dpcoa(humDNAm$samples, sqrt(humDNAm$distances), scan = FALSE, nf = 2)
    dpcoahum
    plot(dpcoahum, csize = 1.5)
    ## Not run:
    data(ecomor)
    ecomor.phylog <- taxo2phylog(ecomor$taxo)
    dpcoaeco <- dpcoa(ecomor$habitat, ecomor.phylog$Wdist, scan = FALSE, nf = 2)
    dpcoaeco
    plot(dpcoaeco, csize = 1.5)
    ## End(Not run)

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