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

View source: R/phylodiversity.R

Standardized effect size of phylogenetic diversity (Faith's PD) in communities.

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` samp ` |
Community data matrix |

` tree ` |
Phylogeny (phylo object) |

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

` runs ` |
Number of randomizations |

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

` include.root ` |
Include distance to root node in calculation of PD (see documentation in |

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

- taxa.labels
Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)

- 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 phylogeny (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 |

`pd.obs` |
Observed PD in community |

`pd.rand.mean` |
Mean PD in null communities |

`pd.rand.sd` |
Standard deviation of PD in null communities |

`pd.obs.rank` |
Rank of observed PD vs. null communities |

`pd.obs.z` |
Standardized effect size of PD vs. null communities (= (pd.obs - pd.rand.mean) / pd.rand.sd) |

`pd.obs.p` |
P-value (quantile) of observed PD vs. null communities (= mpd.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/.

Proches, S., Wilson, J.R.U. and Cowling, R.M. 2006. How much evolutionary history in a 10 x 10m plot? Proceedings of Royal Society of London B, Biological Sciences 273:1143-1148.

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