ses.mnnd: Standardized effect size of MNND

Description

Standardized effect size of mean nearest neighbour distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).

Usage

ses.mnnd(samp, dis, null.model = c("taxa.labels","sample.pool", "phylogeny.pool",
            "independentswap", "trialswap"), runs = 999, iterations = 1000)

Arguments

samp

Community data matrix

dis

Distance matrix (generally a phylogenetic distance matrix)

null.model

Null model to use 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

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
ntaxaNumber of taxa in community
mpd.obsObserved MNND in community
mpd.rand.meanMean MNND in null communities
mpd.rand.sdStandard deviation of MNND in null communities
mpd.obs.rankRank of observed MNND vs. null communities
mpd.obs.zStandardized effect size of MNND vs. null communities (= (mpd.obs - mpd.rand.mean) / mpd.rand.sd, equivalent to -NTI)
mpd.obs.pP-value (quantile) of observed MNND vs. null communities (= mpd.obs.rank / runs + 1)
runsNumber of randomizations

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

Run this code

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