# 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