metricTester (version 1.2.2)

runNulls: Randomize input CDM according to defined null models

Description

Given a prepared nulls.input object, will randomize a community data matrix according to all nulls defined in defineNulls, and return a list of randomized CDMs.

Usage

runNulls(nulls.input, nulls)

Arguments

nulls.input

A prepared nulls.input object, as generated by prepNulls.

nulls

Optional list of named null model functions to use. If invoked, this option will likely be used to run a subset of the defined null models.

Value

A list of matrices. Each matrix is a product of a randomization of the input CDM and one of the nulls from defineNulls.

Details

Currently we are running 9 null models. This function first confirms that the input is of class nulls.input and, if so, then confirms that the nulls to be calculated are in a named list (via checkNulls), then lapplies all null model functions to the input CDM.

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2015. Phylogenetic community structure metrics and null models: a review with new methods and software. bioRxiv 025726.

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 <- prepNulls(tree, cdm)

results <- runNulls(prepped)