Man pages for metricTester
Test Metric and Null Model Statistical Performance

abundanceVectorGenerate regional abundance vector
alphaMetricSimsCalculate alpha metrics under specified tree and community...
arenaTestCalculate SES of each observed metric + null model...
betaErrorCheckerWrapper for summarizing error rates of beta metric...
betaErrorWrapperRead in and calculate type I and II error rates of a set of...
betaLinkerRun spatial simulations, null and beta metric calculations
betaMetricSimsCalculate beta metrics under specified tree and community...
betaMetricsNnullsParallelized function that calculates beta metrics on...
betaMultiLinkerRun multiple simulations and calculations to test beta metric...
calcBetaMetricsCalculate phylogenetic community structure beta metrics
calcFieldCalculate phylogenetic and trait fields
calcMetricsCalculate phylogenetic community structure metrics
centersCalculate weighted centroids
checkBetaMetricsConfirm that the metric functions are in suitable format
checkCDMConfirm that a CDM will run
checkMetricsConfirm that the metric functions are in suitable format
checkNullsConfirm that the null model functions are in suitable format
checkSimulationsConfirm that the spatial simulation functions are in suitable...
competitionArenaSimulate competitive exclusion over multiple generations
defineBetaMetricsOutput all beta metrics as a list of named functions
defineMetricsOutput all metrics as a list of named functions
defineNullsOutput all null models as a list of named functions
defineSimulationsOutput all spatial simulations as a list of named functions
dispersalNullRandomize community data matrix with dispersal null model
distMRCACalculate plot-level distances to most recent common...
errorCheckerWrapper for summarizing randomizations and testing...
evolveTraitsEvolve two traits up a tree
expectationsGenerate expectations for null+metric combinations
FDisCalculate functional dispersion (FDis)
filteringArenaSimulate a community assembled according to habitat filtering
killSomeRemove most closely related individuals
killSomeBigRemove most closely related individuals for large arenas
lengthNonZerosCalculate the species richness of a vector from a CDM
linkerRun spatial simulations, null and metric calculations to test...
makeCDMWrapper for creating a CDM from a spatial simulation result
makeRoadMapCreate a road map for use in FDis-related functions
metricPerformanceSummarize metric performance of a series of summarized...
metricsNnullsParallelized function that calculates metrics on randomized...
modifiedMPDCalculate different versions of abundance-weighted MPD
MRDCalculate mean root distance
multiCDMWrapper for deriving CDMs from the results of multiple...
multiLinkerRun multiple simulations and calculations to test metric +...
newRegionalNullRandomize community data matrix with second-gen regional null...
nullPerformanceSummarize null model performance of a series of summarized...
observedBetaMetricsWrapper for prepping and calculating observed beta metrics
observedMetricsWrapper for prepping and calculating observed metrics
oldRegionalNullRandomize community data matrix with regional null model
phyloFieldCalculate a species' phylogenetic field
plotContentsIdentify individuals contained within a plot
plotOverallOverall per simulation-null-metric plot test
plotPlacerRandomly place plots in arena
plotPlotterPlot simulated plots in arena
plotTestCalculate if single, observed metrics deviate beyond...
prepDataPrep data to test phylogenetic community structure metrics
prepFieldDataPrep data to to calculate phylogenetic fields
prepNullsPrep data for null randomizations
prepSimulationsPrep data for spatial simulations
pscCorrCalculate corrected PSC
randomArenaGenerate a random spatial arena
readInRead in the results of multiple metric/null/simulation tests
reduceRandomizationsReduce randomized results to a manageable list of dataframes
reduceResultsReduce results from multiLinker into a manageable format
relativeCDMConvert absolute abundance matrix to relative abundance
runNullsRandomize input CDM according to defined null models
runSimulationsRun defined spatial simulations
sesFieldCalculate a species' standardized trait field
sesIndivSummary statistics of SES results
sesOverallOverall per simulation-null-metric SES test
sesPhyloFieldCalculate a species' standardized trait field
sesTraitFieldCalculate a species' standardized trait field
settleSomeRandomly settle individuals in a spatial arena
simulateCommGenerate a simulated community data matrix
summariesReturn summary statistics from a data frame of randomized...
summCorrsSummarize correlations among metrics over a result from a...
synthCommCreate synthetic community niche space
traitFieldCalculate a species' trait field
varLandscapeCreate landscapes with varying degrees of heterogeneity
varyXCalculate alpha or beta metrics across a set of parameters
metricTester documentation built on Dec. 16, 2019, 1:20 a.m.