comm.phylo.cor: Correlations between species co-occurrence and phylogenetic distances

Description

Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models

Usage

comm.phylo.cor(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "roij"),
    null.model = c("sample.taxa.labels", "pool.taxa.labels",
        "frequency", "richness", "independentswap","trialswap"), runs = 999, ...)

Arguments

samp

Community data matrix

phylo

Phylogenetic tree

metric

Metric of co-occurrence to use (see species.dist)

null.model

Null model to use: sample.taxa.labels{Shuffle phylogeny tip labels (only within set of taxa present in community data)} pool.taxa.labels{Shuffle phylogeny tip labels (across all taxa included in phylogenetic tree)

runs

Number of runs (randomizations)

...

Additional arguments to randomizeSample

Value

A list with elements:
obs.corrObserved co-occurrence/phylogenetic distance correlation
obs.corr.pP-value of observed correlation (standard P-value for correlation coefficient, not based on comparison with randomizations)
obs.rankRank of observed correlation vs. random
runsNumber of runs (randomizations)
obs.rand.pP-value of observed correlation vs. randomizations (= obs.rank / (runs + 1))
random.corrsA vector of random correlation calculated for each run

References

Cavender-Bares J., D.A. Ackerly, D. Baum and F.A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities, American Naturalist, 163(6):823-843.

Examples

Run this code

data(phylocom)
comm.phylo.cor(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")