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).
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
Currently implemented null models (arguments to null.model):
taxa.labels
Shuffle distance matrix labels (across all taxa included in distance matrix)
richness
Randomize community data matrix abundances within samples (maintains sample species richness)
frequency
Randomize community data matrix abundances within species (maintains species occurence frequency)
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
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
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
Author(s)
Steven Kembel <steve.kembel@gmail.com>
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/.