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

corkdist {ade4} | R Documentation

## 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 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)

[Package ade4 version 1.7-16 Index]