dpcoa: Double principal coordinate analysis

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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 [e-mail]
Stéphane Dray [e-mail]

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
if(adegraphicsLoaded()) {
  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

if(adegraphicsLoaded()) {
  g1 <- plot(dpcoaeco)
} else {
  plot(dpcoaeco)
}

## End(Not run)

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.