as.data.frame.bifrost_search_tuning_grid
                        Convert a fixed-IC search tuning grid to a data
                        frame
as.data.frame.bifrost_search_tuning_selection
                        Convert a tuned search-parameter selection to a
                        data frame
as.data.frame.bifrost_shift_recovery_evaluation
                        Convert a shift-recovery evaluation to a data
                        frame
as.data.frame.bifrost_simulation_study
                        Convert a bifrost simulation study to a data
                        frame
as.data.frame.regime_correlation_pca
                        Convert Regime Correlation PCA Results to Data
                        Frames
as.data.frame.regime_integration_relationships
                        Convert Regime Integration Relationship Results
                        to Data Frames
as.data.frame.regime_module_diagnostics
                        Convert Regime Module Diagnostics to Data
                        Frames
bifrost_example_file    Locate a verified empirical example-data
                        artifact
bootstrap_rate_distribution
                        Bootstrap A Fitted Rate Distribution
compare_shift_magnitudes
                        Compare Rate-Shift Magnitudes
createSimulationTemplate
                        Create an Empirically Calibrated Simulation
                        Template for 'bifrost'
distribution-fit-data-frames
                        Coerce Shift And Distribution Summaries To Data
                        Frames
evaluateShiftRecovery   Evaluate Shift Recovery Against Simulated
                        Ground Truth
fisher_z_transform      Fisher's Z Transformation
fit_rate_distribution   Fit Candidate Distributions To Rates
fit_regime_covariance_runs
                        Fit Post-hoc Regime Covariance Models Across
                        Runs
fit_regime_covariances
                        Fit Independent Post-hoc Regime Covariance
                        Models
fit_waiting_time_distribution
                        Fit Candidate Distributions To Shift Waiting
                        Times
generateViridisColorScale
                        Generate Viridis Color Palette for Ranked
                        Parameters
icTrajectory            Create an Information-Criterion Trajectory
lineage_rates           Compute Weighted Lineage Rates
plot.icTrajectory       Plot an Information-Criterion Trajectory
plot.rateMap            Plot 'rateMap' Objects
plot.rate_distribution_fit
                        Plot A Fitted Rate Distribution
plot.regime_correlation_pca
                        Plot Regime Correlation PCA Results
plot.regime_integration_relationships
                        Plot Regime Rate-Integration Relationships
plot.regime_module_diagnostics
                        Plot Regime Module Diagnostics
plot.shift_magnitude_comparison
                        Plot One Shift-Magnitude Comparison
plot.shift_magnitude_comparison_set
                        Plot A Shift-Magnitude Comparison Set
plot.shift_magnitude_count_set
                        Plot A Shift-Magnitude Count Set
plot.shift_magnitude_counts
                        Plot One Shift Count Or Frequency Comparison
print.bifrost_search    Print method for _'bifrost'_ search results
print.bifrost_search_tuning_grid
                        Print method for fixed-IC search tuning grids
print.bifrost_search_tuning_selection
                        Print method for tuned search-parameter
                        selections
print.bifrost_shift_recovery_evaluation
                        Print method for shift-recovery evaluations
print.bifrost_simulation_study
                        Print method for bifrost simulation studies
print.bifrost_simulation_template
                        Print method for bifrost simulation templates
print.rateMap           Print a 'rateMap' Object
rateMap                 Compute Branchwise Rate Maps Across Runs
rateMapControl          Control Advanced 'rateMap()' Options
rateMapRateFlags        Control Near-Zero and Tail Rate Diagnostics for
                        'rateMap()'
rateMapView             Create a Display View of a 'rateMap' Object
regime_correlation_pca
                        Run PCA on Regime Correlation Structures
regime_integration_pgls
                        Fit the Manuscript-style Regime Integration
                        pGLS
regime_integration_relationships
                        Analyze Rate-Integration Relationships Across
                        Regimes
regime_module_diagnostics
                        Diagnose PCA Axes with User-defined Trait
                        Modules
runFalsePositiveSimulationStudy
                        Run a False-Positive Simulation Study
runSearchTuningGrid     Run a Fixed-IC Search Tuning Grid
runShiftRecoverySimulationStudy
                        Run a Shift-Recovery Simulation Study
searchOptimalConfiguration
                        Search for an Optimal Multi-Regime (Shift)
                        Configuration on a Phylogeny
selectTunedSearchParameters
                        Select Tuned Search Parameters from a Fixed-IC
                        Grid
shift_magnitude_counts
                        Count Inferred Rate Increases And Decreases
shift_magnitude_groups
                        Define Shift-Magnitude Analysis Groups
shift_node_marks        Prepare And Plot Shift Node Marks On A Tree
shift_transitions       Extract Regime Shift Transitions
shift_waiting_times     Compute Waiting Times Between Regime Shifts
simulateNullDataset     Simulate an Empirically Calibrated Null
                        Replicate
simulateShiftedDataset
                        Simulate an Empirically Calibrated Shifted
                        Replicate
summarize_regime_covariance_runs
                        Summarize Post-hoc Regime Covariance Models
                        Across Runs
summarize_regime_covariances
                        Summarize Post-hoc Regime Covariance Matrices
