ses.mpd {picante} | R Documentation |
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).
ses.mpd(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 (see Details section for description) |
runs |
Number of randomizations |
iterations |
Number of iterations to use for each randomization (for independent swap and trial null models) |
Currently implemented null models (arguments to null.model):
A data frame of results for each community
ntaxa |
Number of taxa in community |
mpd.obs |
Observed mpd in community |
mpd.rand.mean |
Mean mpd in null communities |
mpd.rand.sd |
Standard deviation of mpd in null communities |
mpd.obs.rank |
Rank of observed mpd vs. null communities |
mpd.obs.z |
Standardized effect size of mpd vs. null communities (= (mpd.obs - mpd.rand.mean) / mpd.rand.sd, equivalent to -NRI) |
mpd.obs.p |
P-value (quantile) of observed mpd vs. null communities (= mpd.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.mpd(phylocom$sample, cophenetic(phylocom$phylo),null.model="taxa.labels")