R: Quantile regression slopes between species co-occurrence and...
comm.phylo.qr
R Documentation
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
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
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.