comm.phylo.cor {picante} | R Documentation |
Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models
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, ...)
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 |
Currently implemented null models (arguments to null.model):
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 |
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.
data(phylocom) comm.phylo.cor(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")