Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models

1 2 3 | ```
comm.phylo.cor(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "doij"),
null.model = c("sample.taxa.labels", "pool.taxa.labels",
"frequency", "richness", "independentswap","trialswap"), runs = 999, ...)
``` |

`samp` |
Community data matrix |

`phylo` |
Phylogenetic tree |

`metric` |
Metric of co-occurrence to use (see |

`null.model` |
Null model to use (see Details section for description) |

`runs` |
Number of runs (randomizations) |

`...` |
Additional arguments to randomizeMatrix |

Currently implemented null models (arguments to null.model):

- sample.taxa.labels
Shuffle phylogeny tip labels (only within set of taxa present in community data)

- pool.taxa.labels
Shuffle phylogeny tip labels (across all taxa included in phylogenetic tree)

- frequency
Randomize community data matrix abundances within species (maintains species occurence frequency)

- richness
Randomize community data matrix abundances within samples (maintains sample species richness)

- independentswap
Randomize community data matrix maintaining species occurrence frequency and site richnessing using independent swap

- trialswap
Randomize community data matrix maintaining species occurrence frequency and site richnessing using trial swap

A list with elements:

`obs.corr ` |
Observed co-occurrence/phylogenetic distance correlation |

`obs.corr.p` |
P-value of observed correlation (standard P-value for correlation coefficient, not based on comparison with randomizations) |

`obs.rank` |
Rank of observed correlation vs. random |

`runs` |
Number of runs (randomizations) |

`obs.rand.p` |
P-value of observed correlation vs. randomizations (= obs.rank / (runs + 1)) |

`random.corrs` |
A vector of random correlation calculated for each run |

Steven Kembel <steve.kembel@gmail.com>

Cavender-Bares J., D.A. Ackerly, D. Baum and F.A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities, American Naturalist, 163(6):823-843.

1 2 |

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