picante: comm.phylo.cor – R documentation

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comm.phylo.cor

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", "doij"),
    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 randomizeMatrix

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 <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.

Examples

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

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