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metricTester (version 1.3.0)

Test Metric and Null Model Statistical Performance

Description

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

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Install

install.packages('metricTester')

Monthly Downloads

41

Version

1.3.0

License

GPL-3

Issues

0

Pull Requests

0

Stars

8

Forks

3

Maintainer

Eliot Miller

Last Published

July 27th, 2016

Functions in metricTester (1.3.0)

calcBetaMetrics

Calculate phylogenetic community structure beta metrics
betaErrorChecker

Wrapper for summarizing error rates of beta metric randomizations
betaMetricSims

Calculate beta metrics under specified tree and community parameters
arenaTest

Calculate SES of each observed metric + null model combination
betaMultiLinker

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

Parallelized function that calculates beta metrics on randomized matrices
betaLinker

Run spatial simulations, null and beta metric calculations
abundanceVector

Generate regional abundance vector
alphaMetricSims

Calculate alpha metrics under specified tree and community parameters
betaErrorWrapper

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

Simulate competitive exclusion over multiple generations
calcMetrics

Calculate phylogenetic community structure metrics
checkCDM

Confirm that a CDM will run
checkNulls

Confirm that the null model functions are in suitable format
checkSimulations

Confirm that the spatial simulation functions are in suitable format
centers

Calculate weighted centroids
defineBetaMetrics

Output all beta metrics as a list of named functions
calcField

Calculate phylogenetic and trait fields
checkMetrics

Confirm that the metric functions are in suitable format
checkBetaMetrics

Confirm that the metric functions are in suitable format
defineSimulations

Output all spatial simulations as a list of named functions
defineNulls

Output all null models as a list of named functions
evolveTraits

Evolve two traits up a tree
dispersalNull

Randomize community data matrix with dispersal null model
FDis

Calculate functional dispersion (FDis)
defineMetrics

Output all metrics as a list of named functions
filteringArena

Simulate a community assembled according to habitat filtering
distMRCA

Calculate plot-level distances to most recent common ancestors
expectations

Generate expectations for null+metric combinations
errorChecker

Wrapper for summarizing randomizations and testing significance of observed metrics
metricPerformance

Summarize metric performance of a series of summarized simulation results
killSome

Remove most closely related individuals
modifiedMPD

Calculate different versions of abundance-weighted MPD
linker

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

Calculate the species richness of a vector from a CDM
killSomeBig

Remove most closely related individuals for large arenas
metricsNnulls

Parallelized function that calculates metrics on randomized matrices
MRD

Calculate mean root distance
makeCDM

Wrapper for creating a CDM from a spatial simulation result
multiCDM

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

Plot simulated plots in arena
plotTest

Calculate if single, observed metrics deviate beyond expectations
multiLinker

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

Wrapper for prepping and calculating observed beta metrics
plotOverall

Overall per simulation-null-metric plot test
plotPlacer

Randomly place plots in arena
plotContents

Identify individuals contained within a plot
observedMetrics

Wrapper for prepping and calculating observed metrics
nullPerformance

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

Calculate a species' phylogenetic field
readIn

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

Prep data to to calculate phylogenetic fields
sesOverall

Overall per simulation-null-metric SES test
reduceRandomizations

Reduce randomized results to a manageable list of dataframes
sesIndiv

Summary statistics of SES results
relativeCDM

Convert absolute abundance matrix to relative abundance
reduceResults

Reduce results from multiLinker into a manageable format
regionalNull

Randomize community data matrix with regional null model
prepData

Prep data to test phylogenetic community structure metrics
runNulls

Randomize input CDM according to defined null models
summaries

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

Randomly settle individuals in a spatial arena
summCorrs

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

Generate a simulated community data matrix
sesPhyloField

Calculate a species' standardized trait field
sesTraitField

Calculate a species' standardized trait field
prepSimulations

Prep data for spatial simulations
prepNulls

Prep data for null randomizations
varLandscape

Create landscapes with varying degrees of heterogeneity
varyX

Calculate alpha or beta metrics across a set of parameters
pscCorr

Calculate corrected PSC
randomArena

Generate a random spatial arena
sesField

Calculate a species' standardized trait field
runSimulations

Run defined spatial simulations
synthComm

Create synthetic community niche space
traitField

Calculate a species' trait field