ses.pd {picante} | R Documentation |
Standardized effect size of phylogenetic diversity (Faith's PD) in communities.
ses.pd(samp, tree, null.model = c("taxa.labels", "sample.pool", "phylogeny.pool", "independentswap", "trialswap"), runs = 999, iterations = 1000, ...)
samp |
Community data matrix |
tree |
Phylogeny (phylo object) |
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) |
... |
Additional arguments to pd function |
Currently implemented null models (arguments to null.model):
A data frame of results for each community
ntaxa |
Number of taxa in community |
pd.obs |
Observed PD in community |
pd.rand.mean |
Mean PD in null communities |
pd.rand.sd |
Standard deviation of PD in null communities |
pd.obs.rank |
Rank of observed PD vs. null communities |
pd.obs.z |
Standardized effect size of PD vs. null communities (= (pd.obs - pd.rand.mean) / pd.rand.sd) |
pd.obs.p |
P-value (quantile) of observed PD 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/.
Proches, S., Wilson, J.R.U. and Cowling, R.M. 2006. How much evolutionary history in a 10 x 10m plot? Proceedings of Royal Society of London B, Biological Sciences 273:1143-1148.
data(phylocom) ses.pd(phylocom$sample, phylocom$phylo, null.model="taxa.labels", runs=99)