ses.mpd.par: Standardized effect size of MPD

In Russel88/MicEco: Various functions for microbial community data

Standardized effect size of MPD

Description

Parallel calculation of 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.par(
  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

Faster than ses.mpd from picante when there are many samples and taxa.

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

• ntaxaNumber of taxa in community

• mpd.obsObserved mpd in community

• mpd.rand.meanMean mpd in null communities

• mpd.rand.sdStandard deviation of mpd in null communities

• mpd.obs.rankRank of observed mpd vs. null communities

• mpd.obs.zStandardized effect size of mpd vs. null communities (= (mpd.obs - mpd.rand.mean) / mpd.rand.sd, equivalent to -NRI)

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

• runsNumber of randomizations

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