metricTester: Test Metric and Null Model Statistical Performance

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

AuthorEliot Miller, Chris Trisos & Damien Farine
Date of publication2016-07-27 18:57:55
MaintainerEliot Miller <eliot.isaac@gmail.com>
LicenseGPL-3
Version1.3.0
https://github.com/eliotmiller/metricTester

View on CRAN

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

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 +...

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

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

regionalNull: Randomize community data matrix with regional null model

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

Files in this package

metricTester
metricTester/tests
metricTester/tests/testthat.R
metricTester/tests/testthat
metricTester/tests/testthat/test_plot_sampling.R
metricTester/tests/testthat/test_complicated_comm_sims.R
metricTester/tests/testthat/test_calc_metric_null_sim.R
metricTester/tests/testthat/test_post_sim_analyses_by_richness.R
metricTester/tests/testthat/test_define_metric_null_sim.R
metricTester/tests/testthat/test_post_sim_analyses_by_both.R
metricTester/tests/testthat/test_simple_comm_sims.R
metricTester/NAMESPACE
metricTester/NEWS.md
metricTester/R
metricTester/R/varLandscape.R metricTester/R/reduceResults.R metricTester/R/alphaMetricSims.R metricTester/R/betaErrorChecker.R metricTester/R/utils.R metricTester/R/competitionArena.R metricTester/R/defineSimulations.R metricTester/R/plotOverall.R metricTester/R/randomArena.R metricTester/R/runNulls.R metricTester/R/defineMetrics.R metricTester/R/FDis.R metricTester/R/multiLinker.R metricTester/R/relativeCDM.R metricTester/R/runSimulations.R metricTester/R/centers.R metricTester/R/reduceRandomizations.R metricTester/R/synthComm.R metricTester/R/multiCDM.R metricTester/R/modifiedMPD.R metricTester/R/metricPerformance.R metricTester/R/prepNulls.R metricTester/R/plotContents.R metricTester/R/plotPlotter.R metricTester/R/sesTraitField.R metricTester/R/summCorrs.R metricTester/R/makeCDM.R metricTester/R/readIn.R metricTester/R/errorChecker.R metricTester/R/sesOverall.R metricTester/R/summaries.R metricTester/R/evolveTraits.R metricTester/R/calcMetrics.R metricTester/R/settleSome.R metricTester/R/prepData.R metricTester/R/betaMetricsNnulls.R metricTester/R/observedMetrics.R metricTester/R/defineBetaMetrics.R metricTester/R/observedBetaMetrics.R metricTester/R/filteringArena.R metricTester/R/checkBetaMetrics.R metricTester/R/linker.R metricTester/R/phyloField.R metricTester/R/dispersalNull.R metricTester/R/pscCorr.R metricTester/R/checkMetrics.R metricTester/R/distMRCA.R metricTester/R/regionalNull.R metricTester/R/traitField.R metricTester/R/sesField.R metricTester/R/varyX.R metricTester/R/plotTest.R metricTester/R/betaErrorWrapper.R metricTester/R/calcBetaMetrics.R metricTester/R/calcField.R metricTester/R/expectations.R metricTester/R/checkSimulations.R metricTester/R/sesPhyloField.R metricTester/R/killSomeBig.R metricTester/R/prepSimulations.R metricTester/R/checkCDM.R metricTester/R/MRD.R metricTester/R/checkNulls.R metricTester/R/defineNulls.R metricTester/R/nullPerformance.R metricTester/R/prepFieldData.R metricTester/R/metricsNnulls.R metricTester/R/arenaTest.R metricTester/R/plotPlacer.R metricTester/R/simulateComm.R metricTester/R/lengthNonZeros.R metricTester/R/sesIndiv.R metricTester/R/betaLinker.R metricTester/R/betaMetricSims.R
metricTester/R/abundanceVector.r
metricTester/R/betaMultiLinker.R metricTester/R/killSome.R
metricTester/MD5
metricTester/DESCRIPTION
metricTester/man
metricTester/man/prepSimulations.Rd metricTester/man/regionalNull.Rd metricTester/man/summCorrs.Rd metricTester/man/betaMultiLinker.Rd metricTester/man/pscCorr.Rd metricTester/man/readIn.Rd metricTester/man/modifiedMPD.Rd metricTester/man/defineBetaMetrics.Rd metricTester/man/plotPlotter.Rd metricTester/man/makeCDM.Rd metricTester/man/sesPhyloField.Rd metricTester/man/plotPlacer.Rd metricTester/man/summaries.Rd metricTester/man/betaMetricsNnulls.Rd metricTester/man/varLandscape.Rd metricTester/man/MRD.Rd metricTester/man/runSimulations.Rd metricTester/man/defineSimulations.Rd metricTester/man/multiCDM.Rd metricTester/man/evolveTraits.Rd metricTester/man/plotContents.Rd metricTester/man/errorChecker.Rd metricTester/man/checkSimulations.Rd metricTester/man/FDis.Rd metricTester/man/defineMetrics.Rd metricTester/man/alphaMetricSims.Rd metricTester/man/checkMetrics.Rd metricTester/man/metricsNnulls.Rd metricTester/man/competitionArena.Rd metricTester/man/settleSome.Rd metricTester/man/checkBetaMetrics.Rd metricTester/man/multiLinker.Rd metricTester/man/varyX.Rd metricTester/man/reduceResults.Rd metricTester/man/abundanceVector.Rd metricTester/man/expectations.Rd metricTester/man/distMRCA.Rd metricTester/man/betaErrorWrapper.Rd metricTester/man/defineNulls.Rd metricTester/man/nullPerformance.Rd metricTester/man/calcField.Rd metricTester/man/sesTraitField.Rd metricTester/man/prepData.Rd metricTester/man/calcBetaMetrics.Rd metricTester/man/killSome.Rd metricTester/man/plotTest.Rd metricTester/man/observedBetaMetrics.Rd metricTester/man/checkCDM.Rd metricTester/man/centers.Rd metricTester/man/sesIndiv.Rd metricTester/man/relativeCDM.Rd metricTester/man/reduceRandomizations.Rd metricTester/man/betaMetricSims.Rd metricTester/man/betaErrorChecker.Rd metricTester/man/arenaTest.Rd metricTester/man/synthComm.Rd metricTester/man/randomArena.Rd metricTester/man/phyloField.Rd metricTester/man/calcMetrics.Rd metricTester/man/sesField.Rd metricTester/man/linker.Rd metricTester/man/killSomeBig.Rd metricTester/man/checkNulls.Rd metricTester/man/simulateComm.Rd metricTester/man/prepNulls.Rd metricTester/man/observedMetrics.Rd metricTester/man/prepFieldData.Rd metricTester/man/runNulls.Rd metricTester/man/metricPerformance.Rd metricTester/man/dispersalNull.Rd metricTester/man/sesOverall.Rd metricTester/man/traitField.Rd metricTester/man/lengthNonZeros.Rd metricTester/man/filteringArena.Rd metricTester/man/plotOverall.Rd metricTester/man/betaLinker.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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