# dpcoa: Double principal coordinate analysis In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

 dpcoa 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,
RaoDecomp = TRUE)
## S3 method for class 'dpcoa'
plot(x, xax = 1, yax = 2, ...)
## S3 method for class 'dpcoa'
print(x, ...)
## S3 method for class 'dpcoa'
summary(object, ...)

### Arguments

 df a data frame with samples as rows and categories (i.e. species) as columns and abundance or presence-absence as entries. Previous releases of ade4 (<=1.6-2) considered the transposed matrix as argument. dis an object of class dist containing the distances between the categories. scannf a logical value indicating whether the eigenvalues bar plot should be displayed RaoDecomp a logical value indicating whether Rao diversity decomposition should be performed 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, object an object of class dpcoa xax the column number for the x-axis yax the column number for the y-axis ... ... 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 dw a numeric vector containing the weights of the elements (was w1 in previous releases of ade4) lw a numeric vector containing the weights of the samples (was w2 in previous releases of ade4) 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 dls a data frame with the coordinates of the elements (was l1 in previous releases of ade4) li a data frame with the coordinates of the samples (was l2 in previous releases of ade4) c1 a data frame with the scores of the principal axes of the elements

### Author(s)

Daniel Chessel
Sandrine Pavoine pavoine@mnhn.fr
Stéphane Dray stephane.dray@univ-lyon1.fr

### References

Pavoine, S., Dufour, A.B. and Chessel, D. (2004) From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. Journal of Theoretical Biology, 228, 523–537.

### Examples

data(humDNAm)
dpcoahum <- dpcoa(data.frame(t(humDNAm\$samples)), sqrt(humDNAm\$distances), scan = FALSE, nf = 2)
dpcoahum
g1 <- plot(dpcoahum)
} else {
plot(dpcoahum)
}

## Not run:
data(ecomor)
dtaxo <- dist.taxo(ecomor\$taxo)
dpcoaeco <- dpcoa(data.frame(t(ecomor\$habitat)), dtaxo, scan = FALSE, nf = 2)
dpcoaeco