picante: ses.mpd – R documentation

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ses.mpd

Standardized effect size of MPD

Description

Standardized effect size of mean pairwise distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Relative Index (NRI).

Usage

ses.mpd(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

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
`mpd.obs`	Observed mpd in community
`mpd.rand.mean`	Mean mpd in null communities
`mpd.rand.sd`	Standard deviation of mpd in null communities
`mpd.obs.rank`	Rank of observed mpd vs. null communities
`mpd.obs.z`	Standardized effect size of mpd vs. null communities (= (mpd.obs - mpd.rand.mean) / mpd.rand.sd, equivalent to -NRI)
`mpd.obs.p`	P-value (quantile) of observed mpd vs. null communities (= mpd.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.mpd(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