randtest.amova {ade4}R Documentation

Permutation tests on an analysis of molecular variance (in C).

Description

Tests the components of covariance with permutation processes described by Excoffier et al. (1992).

Usage

## S3 method for class 'amova':
randtest(xtest, nrepet = 99, ...)

Arguments

xtest an object of class amova
nrepet the number of permutations
... further arguments passed to or from other methods

Value

returns an object of class krandtest or randtest

Author(s)

Sandrine Pavoine pavoine@biomserv.univ-lyon1.fr

References

Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

Examples

data(humDNAm)
amovahum <- amova(humDNAm$samples, sqrt(humDNAm$distances), humDNAm$structures)
amovahum
randtesthum <- randtest.amova(amovahum, 49)
plot(randtesthum)

Worked out examples


> library(ade4)
> ### Name: randtest.amova
> ### Title: Permutation tests on an analysis of molecular variance (in C).
> ### Aliases: randtest.amova
> ### Keywords: multivariate nonparametric
> 
> ### ** Examples
> 
> data(humDNAm)
> amovahum <- amova(humDNAm$samples, sqrt(humDNAm$distances), humDNAm$structures)
> amovahum
$call
amova(samples = humDNAm$samples, distances = sqrt(humDNAm$distances), 
    structures = humDNAm$structures)

$results
                                Df     Sum Sq    Mean Sq
Between regions                  4  78.238115 19.5595288
Between samples Within regions   5   9.284744  1.8569488
Within samples                 662 316.197379  0.4776395
Total                          671 403.720238  0.6016695

$componentsofcovariance
                                                Sigma          %
Variations  Between regions                0.13380659  21.119144
Variations  Between samples Within regions 0.02213345   3.493396
Variations  Within samples                 0.47763955  75.387459
Total variations                           0.63357958 100.000000

$statphi
                          Phi
Phi-samples-total   0.2461254
Phi-samples-regions 0.0442870
Phi-regions-total   0.2111914

> randtesthum <- randtest.amova(amovahum, 49)
> plot(randtesthum)

> 
> 
> 
>
[Package ade4 Index]