picante: ses.mntd – R documentation

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ses.mntd

Standardized effect size of MNTD

Description

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).

Usage

ses.mntd(samp, dis, null.model = c("taxa.labels", "richness", "frequency",
    "sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
    abundance.weighted=FALSE, runs = 999, iterations = 1000)

Arguments

`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)

Details

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

Value

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

Author(s)

Steven Kembel <steve.kembel@gmail.com>

References

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/.

Examples

data(phylocom)
ses.mntd(phylocom$sample, cophenetic(phylocom$phylo),null.model="taxa.labels")

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