Man pages for bifrost
Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits
| 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... |
| 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... |
| 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.rate_distribution_fit | Plot A Fitted Rate Distribution |
| plot.rateMap | Plot 'rateMap' Objects |
| 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 |
| 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 a 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 |
