corkdist function

Tests of randomization between distances applied to 'kdist' objetcs

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, ...)
## S3 method for class 'corkdist'
plot(x, whichinrow = NULL, whichincol = NULL, 
   gap = 4, nclass = 10,...)

Arguments

• 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
• ...: further arguments passed to or from other methods

Returns

a list of class corkdist containing for each pair of distances an object of class randtest (permutation tests).

Details

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.

Author(s)

Daniel Chessel

Stéphane Dray stephane.dray@univ-lyon1.fr

Examples

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)