picante (version 1.5-1)

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", "doij"),
    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 (see Details section for description)

runs

Number of runs (randomizations)

...

Additional arguments to randomizeMatrix

Value

• A list with elements:
• obs.corr
  Observed co-occurrence/phylogenetic distance correlation
• obs.corr.p
  P-value of observed correlation (standard P-value for correlation coefficient, not based on comparison with randomizations)
• obs.rank
  Rank of observed correlation vs. random
• runs
  Number of runs (randomizations)
• obs.rand.p
  P-value of observed correlation vs. randomizations (= obs.rank / (runs + 1))
• random.corrs
  A vector of random correlation calculated for each run

Details

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

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.

See Also

randomizeMatrix

Examples

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