ade4 (version 1.7-5)

dpcoa: 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)
"plot"(x, xax = 1, yax = 2, ...)
"print" (x, ...)
"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 (

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:

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)