Description Usage Arguments Details Value Author(s) References Examples

Calculates the *phi* statistic on a classified
table of taxa

1 | ```
phi(comm,clustering,minplt=10,p.adjust=FALSE)
``` |

`comm` |
a data.frame with samples as rows and attributes as columns |

`clustering` |
a vector of integers or an object of class ‘clustering’, ‘partition’, or ‘partana’ |

`minplt` |
the minimum number of samples a species must occur in to be included in the calculation |

`p.adjust` |
switch to control adjusting probabilities for simultaneous inference by Hochberg correction |

*phi* is a statistic of agreement between two vectors. In this case
the function calculates the distribution of each species within clusters of a partition,
calculates the *phi* statistic for each species in each cluster.

*φ = \frac{ad - bc}{√{(a+b)\times(c+d)\times(a+c)\times(b+c)}}*

where:

a | sample is in specified type and species is present |

b | sample is not in group and species is present |

c | sample is in type but species is not present |

d | sample is not in type and species is not present |

A data.frame of *φ* values with species as rows and clusters as columns

David W. Roberts droberts@montana.edu

Tichy, L. and M. Chytry. 2006. Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17:809-818.

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