ses.mnnd {picante} | R Documentation |
Standardized effect size of mean nearest neighbour distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).
ses.mnnd(samp, dis, null.model = c("taxa.labels","sample.pool", "phylogeny.pool", "independentswap", "trialswap"), runs = 999, iterations = 1000)
samp |
Community data matrix |
dis |
Distance matrix (generally a phylogenetic distance matrix) |
null.model |
Null model to use
|
runs |
Number of randomizations |
iterations |
Number of iterations to use for each randomization (for independent swap and trial null models) |
A data frame of results for each community
ntaxa |
Number of taxa in community |
mpd.obs |
Observed MNND in community |
mpd.rand.mean |
Mean MNND in null communities |
mpd.rand.sd |
Standard deviation of MNND in null communities |
mpd.obs.rank |
Rank of observed MNND vs. null communities |
mpd.obs.z |
Standardized effect size of MNND vs. null communities (= (mpd.obs - mpd.rand.mean) / mpd.rand.sd, equivalent to -NTI) |
mpd.obs.p |
P-value (quantile) of observed MNND vs. null communities (= mpd.obs.rank / runs + 1) |
runs |
Number of randomizations |
Steve Kembel <skembel@berkeley.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.mnnd(phylocom$sample, cophenetic(phylocom$phylo),null.model="taxa.labels")