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Analysis of molecular variance

amova.Rd

The analysis of molecular variance tests the differences among population and/or groups of populations in a way similar to ANOVA. It includes evolutionary distances among alleles.

Usage

amova(samples, distances, structures)
# S3 method for amova
print(x, full = FALSE, ...)

Arguments

samples

a data frame with haplotypes (or genotypes) as rows, populations as columns and abundance as entries

distances

an object of class dist computed from Euclidean distance. If distances is null, equidistances are used.

structures

a data frame containing, in the jth row and the kth column, the name of the group of level k to which the jth population belongs

x

an object of class amova

full

a logical value indicating whether the original data ('distances', 'samples', 'structures') should be printed

...

further arguments passed to or from other methods

Value

Returns a list of class amova

call

call

results

a data frame with the degrees of freedom, the sums of squares, and the mean squares. Rows represent levels of variability.

componentsofcovariance

a data frame containing the components of covariance and their contribution to the total covariance

statphi

a data frame containing the phi-statistics

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

See also

randtest.amova

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
#>