prepData: Prep data to test phylogenetic community structure metrics

In metricTester: Test Metric and Null Model Statistical Performance

Description

Given a phylo object, and a picante-style community data matrix (sites are rows, species are columns), prepare data for analysis.

Usage

prepData(tree, picante.cdm, optional.dists = NULL)

Arguments

tree	Phylo object.
picante.cdm	A picante-style community data matrix with sites as rows, and species as columns
optional.dists	A symmetric distance matrix can be directly supplied. This option is experimental. Behavior depends on metric being used. If the metric in question relies on the phylogenetic distance matrix from a call to cophenetic(tree), then this optional distance matrix will be inserted instead.

Details

Returns a named list with three elements: the original phylogenetic tree phylogenetic distances among species, and the original picante-style CDM.

Value

An object of class metrics.input

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2016. Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography DOI: 10.1111/ecog.02070

Examples

#simulate tree with birth-death process
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

sim.abundances <- round(rlnorm(5000, meanlog=2, sdlog=1)) + 1

cdm <- simulateComm(tree, richness.vector=10:25, abundances=sim.abundances)

prepped <- prepData(tree, cdm)

metricTester documentation built on Dec. 16, 2019, 1:20 a.m.