amova {ade4} | R Documentation |
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.
amova(samples, distances, structures) ## S3 method for class 'amova' print(x, full = FALSE, ...)
samples |
a data frame with haplotypes (or genotypes) as rows, populations as columns and abundance as entries |
distances |
an object of class |
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 |
full |
a logical value indicating whether the original data ('distances', 'samples', 'structures') should be printed |
... |
further arguments passed to or from other methods |
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 |
Sandrine Pavoine pavoine@mnhn.fr
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.
data(humDNAm) amovahum <- amova(humDNAm$samples, sqrt(humDNAm$distances), humDNAm$structures) amovahum