ses.mntd {picante} | R Documentation |
Standardized effect size of MNTD
Description
Standardized effect size of mean nearest taxon distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).
Usage
ses.mntd(samp, dis, null.model = c("taxa.labels", "richness", "frequency",
"sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted=FALSE, 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) |
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
The metric used by this function has also been referred to as MNND (mean nearest neighbour distance), and the function was named ses.mnnd
in picante versions < 0.7.
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 |
mntd.obs |
Observed MNTD in community |
mntd.rand.mean |
Mean MNTD in null communities |
mntd.rand.sd |
Standard deviation of MNTD in null communities |
mntd.obs.rank |
Rank of observed MNTD vs. null communities |
mntd.obs.z |
Standardized effect size of MNTD vs. null communities (= (mntd.obs - mntd.rand.mean) / mntd.rand.sd, equivalent to -NTI) |
mntd.obs.p |
P-value (quantile) of observed MNTD vs. null communities (= mntd.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/.
See Also
Examples
data(phylocom)
ses.mntd(phylocom$sample, cophenetic(phylocom$phylo),null.model="taxa.labels")