abundanceVector: Generate regional abundance vector

In metricTester: Test Metric and Null Model Statistical Performance

Description

Given a community data matrix of sites by species, extract the column-wise sums (the total number of individuals of each species) and expand to create a regional abundance vector.

Usage

abundanceVector(picante.cdm)

Arguments

picante.cdm

Community data matrix in picante format

Details

Simple function to create a regional abundance vector given a "regional" community data matrix.

Value

A character vector in the form "s1, s1, s1, s2, s2, s3, etc".

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)

abund <- abundanceVector(cdm)

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