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metricTester (version 1.3.6)

Test Metric and Null Model Statistical Performance

Description

Explore the behavior and statistical performance of 13 pre-defined phylogenetic metrics and 11 null models, and of user-defined metrics and null models, as detailed in Miller et al. (2017) .

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install.packages('metricTester')

Monthly Downloads

115

Version

1.3.6

License

GPL-3

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Repository

https://github.com/eliotmiller/metricTester

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Last Published

December 12th, 2019

Functions in metricTester (1.3.6)

abundanceVector

Generate regional abundance vector

alphaMetricSims

Calculate alpha metrics under specified tree and community parameters

Calculate functional dispersion (FDis)

Calculate mean root distance

betaMetricsNnulls

Parallelized function that calculates beta metrics on randomized matrices

Calculate beta metrics under specified tree and community parameters

Calculate phylogenetic and trait fields

betaErrorWrapper

Read in and calculate type I and II error rates of a set of beta metric tests

Run spatial simulations, null and beta metric calculations

betaErrorChecker

Wrapper for summarizing error rates of beta metric randomizations

Calculate phylogenetic community structure metrics

Calculate SES of each observed metric + null model combination

betaMultiLinker

Run multiple simulations and calculations to test beta metric + null performance

calcBetaMetrics

Calculate phylogenetic community structure beta metrics

Calculate plot-level distances to most recent common ancestors

Calculate weighted centroids

Wrapper for summarizing randomizations and testing significance of observed metrics

Confirm that a CDM will run

Confirm that the metric functions are in suitable format

checkSimulations

Confirm that the spatial simulation functions are in suitable format

Run spatial simulations, null and metric calculations to test metric + null performance

checkBetaMetrics

Confirm that the metric functions are in suitable format

Confirm that the null model functions are in suitable format

Randomize community data matrix with dispersal null model

defineSimulations

Output all spatial simulations as a list of named functions

competitionArena

Simulate competitive exclusion over multiple generations

Evolve two traits up a tree

Generate expectations for null+metric combinations

Wrapper for creating a CDM from a spatial simulation result

defineBetaMetrics

Output all beta metrics as a list of named functions

observedBetaMetrics

Wrapper for prepping and calculating observed beta metrics

Parallelized function that calculates metrics on randomized matrices

Calculate different versions of abundance-weighted MPD

Remove most closely related individuals for large arenas

oldRegionalNull

Randomize community data matrix with regional null model

Output all null models as a list of named functions

metricPerformance

Summarize metric performance of a series of summarized simulation results

Output all metrics as a list of named functions

Create a road map for use in FDis-related functions

Calculate a species' phylogenetic field

newRegionalNull

Randomize community data matrix with second-gen regional null model

Run defined spatial simulations

Prep data to to calculate phylogenetic fields

nullPerformance

Summarize null model performance of a series of summarized simulation results

Calculate the species richness of a vector from a CDM

Calculate a species' standardized trait field

Prep data for null randomizations

prepSimulations

Prep data for spatial simulations

Identify individuals contained within a plot

Simulate a community assembled according to habitat filtering

Randomly settle individuals in a spatial arena

Plot simulated plots in arena

Randomly place plots in arena

observedMetrics

Wrapper for prepping and calculating observed metrics

Overall per simulation-null-metric plot test

Calculate corrected PSC

Generate a simulated community data matrix

Convert absolute abundance matrix to relative abundance

Calculate a species' standardized trait field

Create synthetic community niche space

Calculate a species' trait field

Calculate a species' standardized trait field

Generate a random spatial arena

Remove most closely related individuals

Randomize input CDM according to defined null models

Wrapper for deriving CDMs from the results of multiple spatial simulations

Read in the results of multiple metric/null/simulation tests

Return summary statistics from a data frame of randomized metric values

Summarize correlations among metrics over a result from a varyX function

Summary statistics of SES results

Run multiple simulations and calculations to test metric + null performance

Calculate if single, observed metrics deviate beyond expectations

Prep data to test phylogenetic community structure metrics

reduceRandomizations

Reduce randomized results to a manageable list of dataframes

Reduce results from multiLinker into a manageable format

Overall per simulation-null-metric SES test

Create landscapes with varying degrees of heterogeneity

Calculate alpha or beta metrics across a set of parameters