# Permutations to Test for Phylogenetic Signal in Community Composition

### Description

Randomize sample/community data matrices to create null distributions of given metrics

### Usage

1 2 3 | ```
phylostruct(samp, tree, env=NULL, metric=c("psv","psr","pse","psc","sppregs"),
null.model=c("frequency", "richness","independentswap","trialswap"),
runs=100, it=1000, alpha=0.05, fam="binomial")
``` |

### Arguments

`samp` |
community data matrix, species as columns, communities as rows |

`tree` |
phylo tree object or a phylogenetic covariance matrix |

`env` |
environmental data matrix |

`metric` |
if |

`null.model` |
permutation procedure used to create the null distribution, see |

`runs` |
the number of permutations to create the distribution, a rule of thumb is (number of communities)/alpha |

`it` |
the number of swaps for the independent and trial-swap null models, see |

`alpha` |
probability value to compare the observed mean/correlations to a null distribution |

`fam` |
as in |

### Details

The function creates null distributions for the `psd`

set of metrics and for the correlations of `sppregs`

from observed community data sets.

### Value

`metric` |
metric used |

`null.model` |
permutation used |

`runs` |
number of permutations |

`it` |
number of swaps if applicable |

`obs` |
observed mean value of a particular metric or the three observed correlations from |

`mean.null` |
mean(s) of the null distribution(s) |

`quantiles.null` |
quantiles of the null distribution(s) to compare to |

`phylo.structure` |
if |

`nulls` |
null values of the distribution(s) |

### Author(s)

Matthew Helmus mrhelmus@gmail.com

### References

Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007a) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83

Helmus M.R., Savage K., Diebel M.W., Maxted J.T. & Ives A.R. (2007b) Separating the determinants of phylogenetic community structure. Ecology Letters, 10, 917-925

Gotelli N.J. (2000) Null model analysis of species co-occurrence patterns. Ecology, 81, 2606-2621

### See Also

`psd`

,`sppregs`

, `randomizeMatrix`