Correlations between species co-occurrence and phylogenetic distances

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Description

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

Usage

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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

Details

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

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)

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 maintaining species occurrence frequency and site richnessing using independent swap

trialswap

Randomize community data matrix maintaining species occurrence frequency and site richnessing using trial swap

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

Author(s)

Steven Kembel <steve.kembel@gmail.com>

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

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

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