comm.phylo.qr: Quantile regression slopes between species co-occurrence and phylogenetic distances

Description

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

Usage

comm.phylo.qr(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "doij"),
    null.model = c("sample.taxa.labels", "pool.taxa.labels",
        "frequency", "richness", "independentswap","trialswap"), 
        quant = 0.75, runs = 999, show.plot = FALSE, ...)

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)

quant

Quantile of slope to be fit (using rq)

runs

Number of runs (randomizations)

show.plot

Option to display a plot of co-occurrence versus phylogenetic distance with quantile regression slope fit

...

Additional arguments to randomizeMatrix

Value

A list with elements:
obs.qr.interceptObserved co-occurrence/phylogenetic distance quantile regression intercept
obs.qr.slopeObserved co-occurrence/phylogenetic distance quantile regression slope
obs.qr.slope.pP-value of observed quantile regression slope significance versus null model (calculated based on comparison with randomizations)
obs.rankRank of observed quantile regression slope vs. random
runsNumber of runs (randomizations)
random.qr.slopesA vector of quantile regression slopes calculated for each randomization

Details

This function fits a quantile regression of co-occurrence versus phylogenetic distances separating species, and compares observed patterns to the patterns expected under some null model. The quantile regressions are fit using the rq function from the quantreg package.

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. Slingsby, J. A. and G. A. Verboom. 2006. Phylogenetic relatedness limits coexistence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa. The American Naturalist 168:14-27.

Examples

Run this code

data(phylocom)
comm.phylo.qr(phylocom$sample, phylocom$phylo, metric="cij", null.model="sample.taxa.labels", runs=99)

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