picante (version 0.7-1)

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", "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
• 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

Details

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

mpd, randomizeSample

Examples

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