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 <firstname.lastname@example.org>|
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