metricTester (version 1.3.6)

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. If not provided, defines the metrics as all of those in defineMetrics. If only a subset of those is desired, then metrics should take the form of a character vector corresponding to named functions from defineMetrics. The available metrics can be determined by running names(defineMetrics()). Otherwise, if the user would like to define a new metric on the fly, the argument can take the form of a named list of new functions (metrics).

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. 2016. Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography DOI: 10.1111/ecog.02070

Examples

# NOT RUN {
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=c("richness","PSV"))
# }