Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2 3 4 | ```
comm.phylo.qr(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "doij"),
null.model = c("sample.taxa.labels", "pool.taxa.labels",
"frequency", "richness", "independentswap","trialswap"),
quant = 0.75, runs = 999, show.plot = FALSE, ...)
``` |

`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) |

`quant` |
Quantile of slope to be fit (using |

`runs` |
Number of runs (randomizations) |

`show.plot` |
Option to display a plot of co-occurrence versus phylogenetic distance with quantile regression slope fit |

`...` |
Additional arguments to randomizeMatrix |

This function fits a quantile regression of co-occurrence versus phylogenetic distances separating species, and compares observed patterns to the patterns expected under some null model. The quantile regressions are fit using the `rq`

function from the `quantreg`

package.

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.qr.intercept ` |
Observed co-occurrence/phylogenetic distance quantile regression intercept |

`obs.qr.slope ` |
Observed co-occurrence/phylogenetic distance quantile regression slope |

`obs.qr.slope.p` |
P-value of observed quantile regression slope significance versus null model (calculated based on comparison with randomizations) |

`obs.rank` |
Rank of observed quantile regression slope vs. random |

`runs` |
Number of runs (randomizations) |

`random.qr.slopes` |
A vector of quantile regression slopes calculated for each randomization |

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. Slingsby, J. A. and G. A. Verboom. 2006. Phylogenetic relatedness limits coexistence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa. The American Naturalist 168:14-27.

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