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

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

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.

Author

Sandrine Pavoine pavoine@mnhn.fr

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(amovahum, 49)
plot(randtesthum)