ses.mntd {picante}R Documentation

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","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)
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
frequency
Randomize community data matrix abundances within species (maintains species occurence frequency)
richness
Randomize community data matrix abundances within samples (maintains sample species richness)
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 <skembel@uoregon.edu>

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/.

See Also

mntd, randomizeSample

Examples

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

[Package picante version 0.7-2 Index]