corkdist {ade4} | R Documentation |
The mantelkdist and RVkdist functions apply to blocks of distance matrices the mantel.rtest and RV.rtest functions.
mantelkdist (kd, nrepet = 999) RVkdist (kd, nrepet = 999) plot.corkdist (x, whichinrow = NULL, whichincol = NULL, gap = 4, nclass = 10, coeff = 1,...)
kd |
a list of class kdist |
nrepet |
the number of permutations |
x |
an objet of class corkdist , coming from RVkdist or mantelkdist |
whichinrow |
a vector of integers to select the graphs in rows (if NULL all the graphs are computed) |
whichincol |
a vector of integers to select the graphs in columns (if NULL all the graphs are computed) |
gap |
an integer to determinate the space between two graphs |
nclass |
a number of intervals for the histogram |
coeff |
an integer to fit the magnitude of the graph |
... |
further arguments passed to or from other methods |
The corkdist
class has some generic functions print
, plot
and summary
. The plot shows bivariate scatterplots between semi-matrices of distances or histograms of simulated values with an error position.
a list of class corkdist
containing for each pair of distances an object of class randtest
(permutation tests).
Daniel Chessel chessel@biomserv.univ-lyon1.fr
Stéphane Dray dray@biomserv.univ-lyon1.fr
data(friday87) fri.w <- ktab.data.frame(friday87$fau, friday87$fau.blo, tabnames = friday87$tab.names) fri.kc <- lapply(1:10, function(x) dist.binary(fri.w[[x]],10)) names(fri.kc) <- substr(friday87$tab.names,1,4) fri.kd <- kdist(fri.kc) fri.mantel = mantelkdist(kd = fri.kd, nrepet = 999) plot(fri.mantel,1:5,1:5) plot(fri.mantel,1:5,6:10) plot(fri.mantel,6:10,1:5) plot(fri.mantel,6:10,6:10) s.corcircle (dudi.pca(as.data.frame(fri.kd), scan = FALSE)$co) plot(RVkdist(fri.kd),1:5,1:5) data(yanomama) m1 <- mantelkdist(kdist(yanomama),999) m1 summary(m1) plot(m1)