ses.mntd {picante} | R Documentation |
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).
ses.mntd(samp, dis, null.model = c("taxa.labels","sample.pool", "phylogeny.pool", "independentswap", "trialswap"), abundance.weighted=FALSE, runs = 999, iterations = 1000)
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) |
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):
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 |
Steven Kembel <skembel@uoregon.edu>
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/.
data(phylocom) ses.mntd(phylocom$sample, cophenetic(phylocom$phylo),null.model="taxa.labels")