ses.comdist: Standardized effect size of inter-community MPD (betaMPD,...

In Russel88/MicEco: Various functions for microbial community data

Standardized effect size of inter-community MPD (betaMPD, betaNRI)

Description

Standardized effect size of MPD (mean pairwise distance) separating taxa in two communities, a measure of phylogenetic beta diversity

Usage

ses.comdist(
  samp,
  dis,
  null.model = c("taxa.labels", "richness", "frequency", "sample.pool",
    "phylogeny.pool", "independentswap", "trialswap"),
  abundance.weighted = FALSE,
  runs = 999,
  iterations = 1000,
  cores = 1
)

Arguments

samp	Community data matrix with samples as rows
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)
cores	Number of cores to use for parallel computing

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 list of results:

• ntaxa - Number of taxa in community

• comdist.obs - Observed mpd between communities

• comdist.rand.mean - Mean mpd between null communities

• comdist.rand.sd - Standard deviation of mpd between null communities

• comdist.obs.rank - Rank of observed mpd vs. null mpd

• comdist.obs.z - Standardized effect size of mpd vs. null mpd (= (comdist.obs - comdist.rand.mean) / comdist.rand.sd, equivalent to -betaNRI)

• comdist.obs.p - P-value (quantile) of observed mpd vs. null communities (= comdist.obs.rank / runs + 1)

• runs - Number of randomizations

Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.