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. (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(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)

[Package ade4 version 1.4-0 Index]