Description Usage Arguments Details Value

View source: R/ses.comdistnt.R

Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity

1 2 3 4 | ```
ses.comdistnt(samp, dis, null.model = c("taxa.labels", "richness",
"frequency", "sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted = FALSE, exclude.conspecifics = FALSE, runs = 999,
iterations = 1000, cores = 1)
``` |

`samp` |
Community data matrix with samples as rows |

`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) |

`exclude.conspecifics` |
Should conspecific taxa in different communities be exclude from MNTD calculations? (default = FALSE) |

`runs` |
Number of randomizations |

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

`cores` |
Number of cores to use for parallel computing |

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 list of results:

ntaxa - Number of taxa in community

comdistnt.obs - Observed mntd between communities

comdistnt.rand.mean - Mean mntd between null communities

comdistnt.rand.sd - Standard deviation of mntd between null communities

comdistnt.obs.rank - Rank of observed mntd vs. null mntd

comdistnt.obs.z - Standardized effect size of mntd vs. null mntd (= (comdistnt.obs - comdistnt.rand.mean) / comdistnt.rand.sd, equivalent to -betaNTI)

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

runs - Number of randomizations

Russel88/MicEco documentation built on Oct. 24, 2018, 3:07 p.m.

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