metricTester: Test Metric and Null Model Statistical Performance

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

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AuthorEliot Miller, Chris Trisos & Damien Farine
Date of publication2017-02-16 07:13:31
MaintainerEliot Miller <>

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Man pages

abundanceVector: Generate regional abundance vector

alphaMetricSims: Calculate alpha metrics under specified tree and community...

arenaTest: Calculate SES of each observed metric + null model...

betaErrorChecker: Wrapper for summarizing error rates of beta metric...

betaErrorWrapper: Read in and calculate type I and II error rates of a set of...

betaLinker: Run spatial simulations, null and beta metric calculations

betaMetricSims: Calculate beta metrics under specified tree and community...

betaMetricsNnulls: Parallelized function that calculates beta metrics on...

betaMultiLinker: Run multiple simulations and calculations to test beta metric...

calcBetaMetrics: Calculate phylogenetic community structure beta metrics

calcField: Calculate phylogenetic and trait fields

calcMetrics: Calculate phylogenetic community structure metrics

centers: Calculate weighted centroids

checkBetaMetrics: Confirm that the metric functions are in suitable format

checkCDM: Confirm that a CDM will run

checkMetrics: Confirm that the metric functions are in suitable format

checkNulls: Confirm that the null model functions are in suitable format

checkSimulations: Confirm that the spatial simulation functions are in suitable...

competitionArena: Simulate competitive exclusion over multiple generations

defineBetaMetrics: Output all beta metrics as a list of named functions

defineMetrics: Output all metrics as a list of named functions

defineNulls: Output all null models as a list of named functions

defineSimulations: Output all spatial simulations as a list of named functions

dispersalNull: Randomize community data matrix with dispersal null model

distMRCA: Calculate plot-level distances to most recent common...

errorChecker: Wrapper for summarizing randomizations and testing...

evolveTraits: Evolve two traits up a tree

expectations: Generate expectations for null+metric combinations

FDis: Calculate functional dispersion (FDis)

filteringArena: Simulate a community assembled according to habitat filtering

killSome: Remove most closely related individuals

killSomeBig: Remove most closely related individuals for large arenas

lengthNonZeros: Calculate the species richness of a vector from a CDM

linker: Run spatial simulations, null and metric calculations to test...

makeCDM: Wrapper for creating a CDM from a spatial simulation result

makeRoadMap: Create a road map for use in FDis-related functions

metricPerformance: Summarize metric performance of a series of summarized...

metricsNnulls: Parallelized function that calculates metrics on randomized...

modifiedMPD: Calculate different versions of abundance-weighted MPD

MRD: Calculate mean root distance

multiCDM: Wrapper for deriving CDMs from the results of multiple...

multiLinker: Run multiple simulations and calculations to test metric +...

newRegionalNull: Randomize community data matrix with second-gen regional null...

nullPerformance: Summarize null model performance of a series of summarized...

observedBetaMetrics: Wrapper for prepping and calculating observed beta metrics

observedMetrics: Wrapper for prepping and calculating observed metrics

oldRegionalNull: Randomize community data matrix with regional null model

phyloField: Calculate a species' phylogenetic field

plotContents: Identify individuals contained within a plot

plotOverall: Overall per simulation-null-metric plot test

plotPlacer: Randomly place plots in arena

plotPlotter: Plot simulated plots in arena

plotTest: Calculate if single, observed metrics deviate beyond...

prepData: Prep data to test phylogenetic community structure metrics

prepFieldData: Prep data to to calculate phylogenetic fields

prepNulls: Prep data for null randomizations

prepSimulations: Prep data for spatial simulations

pscCorr: Calculate corrected PSC

randomArena: Generate a random spatial arena

readIn: Read in the results of multiple metric/null/simulation tests

reduceRandomizations: Reduce randomized results to a manageable list of dataframes

reduceResults: Reduce results from multiLinker into a manageable format

relativeCDM: Convert absolute abundance matrix to relative abundance

runNulls: Randomize input CDM according to defined null models

runSimulations: Run defined spatial simulations

sesField: Calculate a species' standardized trait field

sesIndiv: Summary statistics of SES results

sesOverall: Overall per simulation-null-metric SES test

sesPhyloField: Calculate a species' standardized trait field

sesTraitField: Calculate a species' standardized trait field

settleSome: Randomly settle individuals in a spatial arena

simulateComm: Generate a simulated community data matrix

summaries: Return summary statistics from a data frame of randomized...

summCorrs: Summarize correlations among metrics over a result from a...

synthComm: Create synthetic community niche space

traitField: Calculate a species' trait field

varLandscape: Create landscapes with varying degrees of heterogeneity

varyX: Calculate alpha or beta metrics across a set of parameters


abundanceVector Man page
alphaMetricSims Man page
arenaTest Man page
betaErrorChecker Man page
betaErrorWrapper Man page
betaLinker Man page
betaMetricSims Man page
betaMetricsNnulls Man page
betaMultiLinker Man page
calcBetaMetrics Man page
calcField Man page
calcMetrics Man page
centers Man page
checkBetaMetrics Man page
checkCDM Man page
checkMetrics Man page
checkNulls Man page
checkSimulations Man page
competitionArena Man page
defineBetaMetrics Man page
defineMetrics Man page
defineNulls Man page
defineSimulations Man page
dispersalNull Man page
distMRCA Man page
errorChecker Man page
evolveTraits Man page
expectations Man page
FDis Man page
filteringArena Man page
killSome Man page
killSomeBig Man page
lengthNonZeros Man page
linker Man page
makeCDM Man page
makeRoadMap Man page
metricPerformance Man page
metricsNnulls Man page
modifiedMPD Man page
MRD Man page
multiCDM Man page
multiLinker Man page
newRegionalNull Man page
nullPerformance Man page
observedBetaMetrics Man page
observedMetrics Man page
oldRegionalNull Man page
phyloField Man page
plotContents Man page
plotOverall Man page
plotPlacer Man page
plotPlotter Man page
plotTest Man page
prepData Man page
prepFieldData Man page
prepNulls Man page
prepSimulations Man page
pscCorr Man page
randomArena Man page
readIn Man page
reduceRandomizations Man page
reduceResults Man page
relativeCDM Man page
runNulls Man page
runSimulations Man page
sesField Man page
sesIndiv Man page
sesOverall Man page
sesPhyloField Man page
sesTraitField Man page
settleSome Man page
simulateComm Man page
summaries Man page
summCorrs Man page
synthComm Man page
traitField Man page
varLandscape Man page
varyX Man page


tests/testthat/test_plot_sampling.R tests/testthat/test_complicated_comm_sims.R tests/testthat/test_calc_metric_null_sim.R tests/testthat/test_post_sim_analyses_by_richness.R tests/testthat/test_define_metric_null_sim.R tests/testthat/test_post_sim_analyses_by_both.R tests/testthat/test_simple_comm_sims.R
R/varLandscape.R R/reduceResults.R R/alphaMetricSims.R R/betaErrorChecker.R R/utils.R R/competitionArena.R R/defineSimulations.R R/plotOverall.R R/randomArena.R R/runNulls.R R/defineMetrics.R R/FDis.R R/multiLinker.R R/relativeCDM.R R/runSimulations.R R/centers.R R/reduceRandomizations.R R/synthComm.R R/multiCDM.R R/modifiedMPD.R R/metricPerformance.R R/prepNulls.R R/plotContents.R R/plotPlotter.R R/sesTraitField.R R/summCorrs.R R/makeCDM.R R/readIn.R R/errorChecker.R R/sesOverall.R R/summaries.R R/evolveTraits.R R/calcMetrics.R R/settleSome.R R/prepData.R R/betaMetricsNnulls.R R/observedMetrics.R R/defineBetaMetrics.R R/observedBetaMetrics.R R/filteringArena.R R/checkBetaMetrics.R R/linker.R R/phyloField.R R/dispersalNull.R R/pscCorr.R R/oldRegionalNull.R R/checkMetrics.R R/distMRCA.R R/makeRoadMap.R R/traitField.R R/sesField.R R/varyX.R R/plotTest.R R/betaErrorWrapper.R R/calcBetaMetrics.R R/calcField.R R/expectations.R R/checkSimulations.R R/sesPhyloField.R R/killSomeBig.R R/prepSimulations.R R/checkCDM.R R/MRD.R R/checkNulls.R R/defineNulls.R R/nullPerformance.R R/newRegionalNull.R R/prepFieldData.R R/metricsNnulls.R R/arenaTest.R R/plotPlacer.R R/simulateComm.R R/lengthNonZeros.R R/sesIndiv.R R/betaLinker.R R/betaMetricSims.R R/abundanceVector.r R/betaMultiLinker.R R/killSome.R
man/prepSimulations.Rd man/summCorrs.Rd man/oldRegionalNull.Rd man/betaMultiLinker.Rd man/pscCorr.Rd man/readIn.Rd man/modifiedMPD.Rd man/defineBetaMetrics.Rd man/plotPlotter.Rd man/makeCDM.Rd man/sesPhyloField.Rd man/plotPlacer.Rd man/summaries.Rd man/betaMetricsNnulls.Rd man/varLandscape.Rd man/MRD.Rd man/runSimulations.Rd man/defineSimulations.Rd man/multiCDM.Rd man/evolveTraits.Rd man/plotContents.Rd man/errorChecker.Rd man/checkSimulations.Rd man/FDis.Rd man/defineMetrics.Rd man/alphaMetricSims.Rd man/checkMetrics.Rd man/metricsNnulls.Rd man/competitionArena.Rd man/settleSome.Rd man/checkBetaMetrics.Rd man/multiLinker.Rd man/varyX.Rd man/reduceResults.Rd man/abundanceVector.Rd man/expectations.Rd man/distMRCA.Rd man/betaErrorWrapper.Rd man/defineNulls.Rd man/nullPerformance.Rd man/calcField.Rd man/sesTraitField.Rd man/prepData.Rd man/calcBetaMetrics.Rd man/killSome.Rd man/plotTest.Rd man/observedBetaMetrics.Rd man/makeRoadMap.Rd man/checkCDM.Rd man/centers.Rd man/sesIndiv.Rd man/relativeCDM.Rd man/reduceRandomizations.Rd man/betaMetricSims.Rd man/betaErrorChecker.Rd man/arenaTest.Rd man/synthComm.Rd man/randomArena.Rd man/phyloField.Rd man/calcMetrics.Rd man/sesField.Rd man/linker.Rd man/killSomeBig.Rd man/checkNulls.Rd man/newRegionalNull.Rd man/simulateComm.Rd man/prepNulls.Rd man/observedMetrics.Rd man/prepFieldData.Rd man/runNulls.Rd man/metricPerformance.Rd man/dispersalNull.Rd man/sesOverall.Rd man/traitField.Rd man/lengthNonZeros.Rd man/filteringArena.Rd man/plotOverall.Rd man/betaLinker.Rd

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