metricTester (version 1.2.2)

observedMetrics: Wrapper for prepping and calculating observed metrics

Description

Given a cdm and phylogeny, this function preps the data and calculates metrics of the user's choice

Usage

observedMetrics(tree, picante.cdm, metrics)

Arguments

tree

Phylo object

picante.cdm

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

metrics

Optional list of named metric functions to use. If invoked, this option will likely be used to run a subset of the defined metrics. Defaults to all metrics defined in defineMetrics()

Value

A data frame with the species richness and calculated phylogenetic community structure metrics for all input plots from the CDM.

Details

A simple wrapper function to quickly prep data and calculate observed metrics.

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

tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

#prep the data for the simulation
prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=2, 
	length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
	competition.iterations=3)

positions <- randomArena(prepped)

tempCDM <- makeCDM(positions, 15, 30)

results <- observedMetrics(tree=tree, picante.cdm=tempCDM$picante.cdm)

#example of how to pass specific metrics to be calculated (always use at least 
#richness). not run

#results <- observedMetrics(tree=tree, picante.cdm=tempCDM$picante.cdm, 
#metrics=list("richness"=metricTester:::my_richness,"PSV"=metricTester:::my_psv))