picante (version 0.6-1)

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"), 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)

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")