picante: comdistnt – R documentation

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comdistnt

Calculates inter-community mean nearest taxon distance

Description

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

Usage

comdistnt(comm, dis, abundance.weighted = FALSE, exclude.conspecifics = FALSE)

Arguments

`comm`	Community data matrix
`dis`	Interspecific distance matrix
`abundance.weighted`	Should mean nearest taxon distances from each species to species in the other community be weighted by species abundance? (default = FALSE)
`exclude.conspecifics`	Should conspecific taxa in different communities be exclude from MNTD calculations? (default = FALSE)

Details

This metric has also been referred to as MNND (mean nearest neighbour distance).

This function calculates a measure of phylogenetic beta diversity: the average phylogenetic distance to the most similar taxon or individual in the other community for taxa or individuals in two communities.

Value

Distance object of MNTD values separating each pair of communities.

Author(s)

Steven Kembel <steve.kembel@gmail.com>

References

C.O. Webb, D.D. Ackerly, and S.W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 18:2098-2100.

Examples

data(phylocom)
comdistnt(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted=FALSE)

picante

Integrating Phylogenies and Ecology

v1.8.2

GPL-2

Authors

Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>

Initial release

2020-06-08