corkdist: Tests of randomization between distances applied to 'kdist'...

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tests of randomization between distances applied to 'kdist' objetcs

Description

The mantelkdist and RVkdist functions apply to blocks of distance matrices the mantel.rtest and RV.rtest functions.

Usage

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

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.

Value

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

Author(s)

Daniel Chessel
Stéphane Dray [e-mail]

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)

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.