Description Usage Arguments Details Value

View source: R/ses.comdistnt2.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.comdistnt2(samp, dis, method = "quasiswap", fixedmar = "both",
shuffle = "both", strata = NULL, mtype = "count", burnin = 0,
thin = 1, abundance.weighted = FALSE, exclude.conspecifics = FALSE,
runs = 999, cores = 1)
``` |

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

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

`method` |
Character for method used for the swap algorithm ("swap", "tswap", "quasiswap", "backtrack"). If NULL no swap algorithm is applied (uses permatfull from vegan). If mtype="count" the "quasiswap", "swap", "swsh" and "abuswap" methods are available (see details). |

`fixedmar` |
Character, stating which of the row/column sums should be preserved ("none", "rows", "columns", "both"). |

`shuffle` |
Character, indicating whether individuals ("ind"), samples ("samp") or both ("both") should be shuffled, see details. |

`strata` |
Numeric vector or factor with length same as nrow(m) for grouping rows within strata for restricted permutations. Unique values or levels are used. |

`mtype` |
Matrix data type, either "count" for count data, or "prab" for presence-absence type incidence data. |

`burnin` |
Number of null communities discarded before proper analysis in sequential ("swap", "tswap") methods. |

`thin` |
Number of discarded permuted matrices between two evaluations in sequential ("swap", "tswap") methods. |

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

`runs` |
Number of randomizations |

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

See permat (vegan) for detailed options

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

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