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

Standardized effect size of mean nearest taxon distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).

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` samp ` |
Community data matrix |

` dis ` |
Distance matrix (generally a phylogenetic distance matrix) |

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

` abundance.weighted ` |
Should mean nearest taxon distances for each species be weighted by species abundance? (default = FALSE) |

` runs ` |
Number of randomizations |

` iterations ` |
Number of iterations to use for each randomization (for independent swap and trial null models) |

The metric used by this function has also been referred to as MNND (mean nearest neighbour distance), and the function was named `ses.mnnd`

in picante versions < 0.7.

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

- taxa.labels
Shuffle distance matrix labels (across all taxa included in distance matrix)

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

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

- sample.pool
Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability

- phylogeny.pool
Randomize community data matrix by drawing species from pool of species occurring in the distance matrix (phylogeny pool) with equal probability

- independentswap
Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness

- trialswap
Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness

A data frame of results for each community

`ntaxa` |
Number of taxa in community |

`mntd.obs` |
Observed MNTD in community |

`mntd.rand.mean` |
Mean MNTD in null communities |

`mntd.rand.sd` |
Standard deviation of MNTD in null communities |

`mntd.obs.rank` |
Rank of observed MNTD vs. null communities |

`mntd.obs.z` |
Standardized effect size of MNTD vs. null communities (= (mntd.obs - mntd.rand.mean) / mntd.rand.sd, equivalent to -NTI) |

`mntd.obs.p` |
P-value (quantile) of observed MNTD vs. null communities (= mntd.obs.rank / runs + 1) |

`runs` |
Number of randomizations |

Steven Kembel <steve.kembel@gmail.com>

Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. http://www.phylodiversity.net/phylocom/.

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