comm.phylo.cor {picante}R Documentation

Correlations between species co-occurrence and phylogenetic distances

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", "roij"),
    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 randomizeSample

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 <skembel@uoregon.edu>

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

randomizeSample

Examples

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

[Package picante version 0.6-1 Index]