picante: comm.phylo.qr – R documentation

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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

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):

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.qr.intercept`	Observed co-occurrence/phylogenetic distance quantile regression intercept
`obs.qr.slope`	Observed co-occurrence/phylogenetic distance quantile regression slope
`obs.qr.slope.p`	P-value of observed quantile regression slope significance versus null model (calculated based on comparison with randomizations)
`obs.rank`	Rank of observed quantile regression slope vs. random
`runs`	Number of runs (randomizations)
`random.qr.slopes`	A vector of quantile regression slopes calculated for each randomization

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. 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

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

picante

Integrating Phylogenies and Ecology

v1.8.2

GPL-2

Authors

Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>

Initial release

2020-06-08