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| abundanceVector | Generate regional abundance vector |
| alphaMetricSims | Calculate alpha metrics under specified tree and community parameters |
| arenaTest | Calculate SES of each observed metric + null model combination |
| betaErrorChecker | Wrapper for summarizing error rates of beta metric randomizations |
| betaErrorWrapper | Read in and calculate type I and II error rates of a set of beta metric tests |
| betaLinker | Run spatial simulations, null and beta metric calculations |
| betaMetricSims | Calculate beta metrics under specified tree and community parameters |
| betaMetricsNnulls | Parallelized function that calculates beta metrics on randomized matrices |
| betaMultiLinker | Run multiple simulations and calculations to test beta metric + null performance |
| 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 format |
| 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 ancestors |
| errorChecker | Wrapper for summarizing randomizations and testing significance of observed metrics |
| 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 metric + null performance |
| 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 simulation results |
| metricsNnulls | Parallelized function that calculates metrics on randomized matrices |
| modifiedMPD | Calculate different versions of abundance-weighted MPD |
| MRD | Calculate mean root distance |
| multiCDM | Wrapper for deriving CDMs from the results of multiple spatial simulations |
| multiLinker | Run multiple simulations and calculations to test metric + null performance |
| newRegionalNull | Randomize community data matrix with second-gen regional null model |
| nullPerformance | Summarize null model performance of a series of summarized simulation results |
| 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 expectations |
| 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 metric values |
| summCorrs | Summarize correlations among metrics over a result from a varyX function |
| 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 |