Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

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Documentation for package ‘bifrost’ version 0.2.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

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.rate_distribution_fit	Coerce Shift And Distribution Summaries To Data Frames
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
as.data.frame.shift_magnitude_comparison	Coerce Shift And Distribution Summaries To Data Frames
as.data.frame.shift_magnitude_comparison_set	Coerce Shift And Distribution Summaries To Data Frames
as.data.frame.shift_magnitude_counts	Coerce Shift And Distribution Summaries To Data Frames
as.data.frame.shift_magnitude_count_set	Coerce Shift And Distribution Summaries To Data Frames
as.data.frame.shift_node_marks	Prepare And Plot Shift Node Marks On A Tree
as.data.frame.waiting_time_distribution_fit	Coerce Shift And Distribution Summaries 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_covariances	Fit Independent Post-hoc Regime Covariance Models
fit_regime_covariance_runs	Fit Post-hoc Regime Covariance Models Across Runs
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_counts	Plot One Shift Count Or Frequency Comparison
plot.shift_magnitude_count_set	Plot A Shift-Magnitude Count Set
plot.shift_node_marks	Prepare And Plot Shift Node Marks On A Tree
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_covariances	Summarize Post-hoc Regime Covariance Matrices
summarize_regime_covariance_runs	Summarize Post-hoc Regime Covariance Models Across Runs