amova | 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.

`randtest.amova`

data(humDNAm) amovahum <- amova(humDNAm$samples, sqrt(humDNAm$distances), humDNAm$structures) amovahum

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