dpcoa {ade4} | R Documentation |
Performs a double principal coordinate analysis
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, ...)
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 |
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 |
Daniel Chessel chessel@biomserv.univ-lyon1.fr
Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr
Anne B Dufour dufour@biomserv.univ-lyon1.fr
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.
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)