Test Metric and Null Model Statistical Performance

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 |

makeRoadMap | Create a road map for use in FDis-related functions |

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 +... |

newRegionalNull | Randomize community data matrix with second-gen regional null... |

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 |

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... |

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... |

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 |

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