Analysis of molecular variance

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 class '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

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
#>