ses.pd {picante}R Documentation

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

Details

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

taxa.labels
Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)
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
frequency
Randomize community data matrix abundances within species (maintains species occurence frequency)
richness
Randomize community data matrix abundances within samples (maintains sample species richness)
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

Value

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

Author(s)

Steven Kembel <skembel@uoregon.edu>

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.

See Also

pd, randomizeSample

Examples

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

[Package picante version 0.7-2 Index]