ses.pd: Standardized effect size of PD

Description

Standardized effect size of phylogenetic diversity (Faith's PD) in communities.

Usage

ses.pd(samp, tree, null.model = c("taxa.labels", "sample.pool",
            "phylogeny.pool", "independentswap", "trialswap"),
            runs = 999, iterations = 1000, ...)

Arguments

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

Value

A data frame of results for each community
ntaxaNumber of taxa in community
pd.obsObserved PD in community
pd.rand.meanMean PD in null communities
pd.rand.sdStandard deviation of PD in null communities
pd.obs.rankRank of observed PD vs. null communities
pd.obs.zStandardized effect size of PD vs. null communities (= (pd.obs - pd.rand.mean) / pd.rand.sd)
pd.obs.pP-value (quantile) of observed PD vs. null communities (= mpd.obs.rank / runs + 1)
runsNumber of randomizations

Details

Currently implemented null models (arguments to null.model): [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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/.

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.

Examples

Run this code

data(phylocom)
ses.pd(phylocom$sample, phylocom$phylo, null.model="taxa.labels", runs=99)

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