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

Author | Eliot Miller, Chris Trisos & Damien Farine |

Date of publication | 2016-07-27 18:57:55 |

Maintainer | Eliot Miller <eliot.isaac@gmail.com> |

License | GPL-3 |

Version | 1.3.0 |

https://github.com/eliotmiller/metricTester |

**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

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
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