comm.phylo.qr {picante} | R Documentation |
Calculates measures of community phylogenetic structure (quantile regression between co-occurrence and phylogenetic distance) to patterns expected under various null models
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, ...)
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 randomizeSample |
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):
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 |
Steven Kembel <skembel@uoregon.edu>
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.
data(phylocom) comm.phylo.qr(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")