ses.pd: Standardized effect size of PD
In picante: Integrating Phylogenies and Ecology

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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)
`include.root`	Include distance to root node in calculation of PD (see documentation in `pd` function

Currently implemented null models (arguments to null.model):

taxa.labels: Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)
richness: Randomize community data matrix abundances within samples (maintains sample species richness)
frequency: Randomize community data matrix abundances within species (maintains species occurence frequency)
sample.pool: Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability
phylogeny.pool: Randomize community data matrix by drawing species from pool of species occurring in the phylogeny (phylogeny pool) with equal probability
independentswap: Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness
trialswap: Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness

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 <steve.kembel@gmail.com>

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.

pd, randomizeMatrix