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metricTester (version 1.0.0)

Test Metric and Null Model Statistical Performance

Description

Explore the behavior and performance of phylogenetic metrics and null models.

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Version

Install

install.packages('metricTester')

Monthly Downloads

44

Version

1.0.0

License

GPL-3

Issues

1

Pull Requests

0

Stars

9

Forks

3

Maintainer

Eliot Miller

Last Published

March 29th, 2016

Functions in metricTester (1.0.0)

alphaMetricSims

Calculate alpha metrics under specified tree and community parameters
checkBetaMetrics

Confirm that the metric functions are in suitable format
betaMultiLinker

Run multiple simulations and calculations to test beta metric + null performance
betaLinker

Run spatial simulations, null and beta metric calculations
prepNulls

Prep data for null randomizations
reduceRandomizations

Reduce randomized results to a manageable list of dataframes
sesOverall

Overall per simulation-null-metric SES test
betaMetricsNnulls

Parallelized function that calculates beta metrics on randomized matrices
checkNulls

Confirm that the null model functions are in suitable format
evolveTraits

Evolve two traits up a tree
defineMetrics

Output all metrics as a list of named functions
defineNulls

Output all null models as a list of named functions
defineBetaMetrics

Output all beta metrics as a list of named functions
plotOverall

Overall per simulation-null-metric plot test
plotContents

Identify individuals contained within a plot
checkSimulations

Confirm that the spatial simulation functions are in suitable format
dispersalNull

Randomize community data matrix with dispersal null model
pscCorr

Calculate corrected PSC
sesIndiv

Summary statistics of SES results
lengthNonZeros

Calculate the species richness of a vector from a CDM
linker

Run spatial simulations, null and metric calculations to test metric + null performance
makeCDM

Wrapper for creating a CDM from a spatial simulation result
plotPlacer

Randomly place plots in arena
observedBetaMetrics

Wrapper for prepping and calculating observed beta metrics
prepData

Prep data to test phylogenetic community structure metrics
randomArena

Generate a random spatial arena
sesSingle

Summary of results from a single iteration
runNulls

Randomize input CDM according to defined null models
arenaTest

Calculate SES of each observed metric + null model combination
abundanceVector

Generate regional abundance vector
relativeCDM

Convert absolute abundance matrix to relative abundance
killSome

Remove most closely related individuals
expectations

Generate expectations for null+metric combinations
multiCDM

Wrapper for deriving CDMs from the results of multiple spatial simulations
competitionArena

Simulate competitive exclusion over multiple generations
runSimulations

Run defined spatial simulations
nullPerformance

Summarize null model performance of a series of summarized simulation results
summCorrs

Summarize correlations among metrics over a result from a varyX function
calcMetrics

Calculate phylogenetic community structure metrics
sesTraitField

Calculate a species' standardized trait field
simulateComm

Generate a simulated community data matrix
observedMetrics

Wrapper for prepping and calculating observed metrics
defineSimulations

Output all spatial simulations as a list of named functions
betaErrorChecker

Wrapper for summarizing error rates of beta metric randomizations
plotTest

Calculate if single, observed metrics deviate beyond expectations
betaErrorWrapper

Read in and calculate type I and II error rates of a set of beta metric tests
modifiedMPD

Calculate different versions of abundance-weighted MPD
killSomeBig

Remove most closely related individuals for large arenas
readIn

Read in the results of multiple metric/null/simulation tests
reduceResults

Reduce results from multiLinker into a manageable format
betaMetricSims

Calculate beta metrics under specified tree and community parameters
varyX

Calculate alpha or beta metrics across a set of parameters
traitField

Calculate a species' trait field
filteringArena

Simulate a community assembled according to habitat filtering
metricPerformance

Summarize metric performance of a series of summarized simulation results
multiLinker

Run multiple simulations and calculations to test metric + null performance
prepSimulations

Prep data for spatial simulations
summaries

Return summary statistics from a data frame of randomized metric values
checkMetrics

Confirm that the metric functions are in suitable format
calcBetaMetrics

Calculate phylogenetic community structure beta metrics
metricsNnulls

Parallelized function that calculates metrics on randomized matrices
plotPlotter

Plot simulated plots in arena
sesPhyloField

Calculate a species' standardized trait field
checkCDM

Confirm that a CDM will run
errorChecker

Wrapper for summarizing randomizations and testing significance of observed metrics
phyloField

Calculate a species' phylogenetic field
regionalNull

Randomize community data matrix with regional null model
settleSome

Randomly settle individuals in a spatial arena