ses.comdistnt | R Documentation |
Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity
ses.comdistnt( samp, dis, null.model = c("taxa.labels", "richness", "frequency", "sample.pool", "phylogeny.pool", "independentswap", "trialswap"), abundance.weighted = FALSE, exclude.conspecifics = FALSE, runs = 999, iterations = 1000, cores = 1 )
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) |
exclude.conspecifics |
Should conspecific taxa in different communities be exclude from MNTD calculations? (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 |
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
A list of results:
ntaxa - Number of taxa in community
comdistnt.obs - Observed mntd between communities
comdistnt.rand.mean - Mean mntd between null communities
comdistnt.rand.sd - Standard deviation of mntd between null communities
comdistnt.obs.rank - Rank of observed mntd vs. null mntd
comdistnt.obs.z - Standardized effect size of mntd vs. null mntd (= (comdistnt.obs - comdistnt.rand.mean) / comdistnt.rand.sd, equivalent to -betaNTI)
comdistnt.obs.p - P-value (quantile) of observed mntd vs. null communities (= comdistnt.obs.rank / runs + 1)
runs - Number of randomizations
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