metricTester: Test Metric and Null Model Statistical Performance

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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
URLs

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