metricTester (version 1.3.6)

prepNulls: Prep data for null randomizations

Description

Given a phylo object, a picante-style community data matrix (sites are rows, species are columns), and an optional vector of regional abundance, prepare data for randomizations.

Usage

prepNulls(tree, picante.cdm, regional.abundance = NULL,
  distances.among = NULL)

Arguments

tree

Phylo object

picante.cdm

A picante-style community data matrix with sites as rows, and species as columns

regional.abundance

A character vector in the form "s1, s1, s1, s2, s2, s3, etc". Optional, will be generated from the input CDM if not provided.

distances.among

An optional symmetric distance matrix describing the distances among plots/etc, for use with null models like the dispersal null.

Value

A list of class nulls.input

Details

Returns a named list with four elements: the original phylogenetic tree, the original picante-style CDM, a spacodi-style CDM, and vector of regional abundance.

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

# NOT RUN {
#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)
# }