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

In picante: R tools for integrating phylogenies and ecology

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

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 <[e-mail]>

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")

picante documentation built on May 2, 2019, 6:30 p.m.