picante (version 0.7-1)

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","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)

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

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): [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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")