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metricTester (version 1.2.2)

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

1.2.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

8

Forks

3

Maintainer

Eliot Miller

Last Published

June 25th, 2016

Functions in metricTester (1.2.2)

alphaMetricSims

Calculate alpha metrics under specified tree and community parameters
calcBetaMetrics

Calculate phylogenetic community structure beta metrics
betaMetricSims

Calculate beta metrics under specified tree and community parameters
abundanceVector

Generate regional abundance vector
betaMetricsNnulls

Parallelized function that calculates beta metrics on randomized matrices
betaMultiLinker

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

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

Run spatial simulations, null and beta metric calculations
arenaTest

Calculate SES of each observed metric + null model combination
betaErrorChecker

Wrapper for summarizing error rates of beta metric randomizations
calcField

Calculate phylogenetic and trait fields
checkNulls

Confirm that the null model functions are in suitable format
checkMetrics

Confirm that the metric functions are in suitable format
checkSimulations

Confirm that the spatial simulation functions are in suitable format
checkCDM

Confirm that a CDM will run
competitionArena

Simulate competitive exclusion over multiple generations
defineBetaMetrics

Output all beta metrics as a list of named functions
calcMetrics

Calculate phylogenetic community structure metrics
centers

Calculate weighted centroids
checkBetaMetrics

Confirm that the metric functions are in suitable format
defineSimulations

Output all spatial simulations as a list of named functions
evolveTraits

Evolve two traits up a tree
distMRCA

Calculate plot-level distances to most recent common ancestors
errorChecker

Wrapper for summarizing randomizations and testing significance of observed metrics
defineMetrics

Output all metrics as a list of named functions
defineNulls

Output all null models as a list of named functions
filteringArena

Simulate a community assembled according to habitat filtering
FDis

Calculate functional dispersion (FDis)
expectations

Generate expectations for null+metric combinations
dispersalNull

Randomize community data matrix with dispersal null model
linker

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

Calculate different versions of abundance-weighted MPD
MRD

Calculate mean root distance
killSome

Remove most closely related individuals
metricsNnulls

Parallelized function that calculates metrics on randomized matrices
killSomeBig

Remove most closely related individuals for large arenas
lengthNonZeros

Calculate the species richness of a vector from a CDM
multiCDM

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

Wrapper for creating a CDM from a spatial simulation result
metricPerformance

Summarize metric performance of a series of summarized simulation results
plotContents

Identify individuals contained within a plot
observedBetaMetrics

Wrapper for prepping and calculating observed beta metrics
plotOverall

Overall per simulation-null-metric plot test
observedMetrics

Wrapper for prepping and calculating observed metrics
plotTest

Calculate if single, observed metrics deviate beyond expectations
plotPlacer

Randomly place plots in arena
plotPlotter

Plot simulated plots in arena
multiLinker

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

Prep data for null randomizations
prepSimulations

Prep data for spatial simulations
pscCorr

Calculate corrected PSC
reduceRandomizations

Reduce randomized results to a manageable list of dataframes
randomArena

Generate a random spatial arena
prepData

Prep data to test phylogenetic community structure metrics
prepFieldData

Prep data to to calculate phylogenetic fields
reduceResults

Reduce results from multiLinker into a manageable format
regionalNull

Randomize community data matrix with regional null model
sesSingle

Summary of results from a single iteration
sesPhyloField

Calculate a species' standardized trait field
sesIndiv

Summary statistics of SES results
simulateComm

Generate a simulated community data matrix
summaries

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

Overall per simulation-null-metric SES test
relativeCDM

Convert absolute abundance matrix to relative abundance
runNulls

Randomize input CDM according to defined null models
traitField

Calculate a species' trait field
varyX

Calculate alpha or beta metrics across a set of parameters
sesTraitField

Calculate a species' standardized trait field
settleSome

Randomly settle individuals in a spatial arena
sesField

Calculate a species' standardized trait field
summCorrs

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

Run defined spatial simulations
synthComm

Create synthetic community niche space