as.data.frame.bifrost_search_tuning_grid	as.data.frame.bifrost_search_tuning_grid
as.data.frame.bifrost_search_tuning_selection	as.data.frame.bifrost_search_tuning_selection
as.data.frame.bifrost_shift_recovery_evaluation	as.data.frame.bifrost_shift_recovery_evaluation
as.data.frame.bifrost_simulation_study	as.data.frame.bifrost_simulation_study
as.data.frame.rate_distribution_fit	distribution-fit-data-frames
as.data.frame.regime_correlation_pca	as.data.frame.regime_correlation_pca
as.data.frame.regime_integration_relationships	as.data.frame.regime_integration_relationships
as.data.frame.regime_module_diagnostics	as.data.frame.regime_module_diagnostics
as.data.frame.shift_magnitude_comparison	distribution-fit-data-frames
as.data.frame.shift_magnitude_comparison_set	distribution-fit-data-frames
as.data.frame.shift_magnitude_counts	distribution-fit-data-frames
as.data.frame.shift_magnitude_count_set	distribution-fit-data-frames
as.data.frame.shift_node_marks	shift_node_marks
as.data.frame.waiting_time_distribution_fit	distribution-fit-data-frames
bifrost_example_file	bifrost_example_file
bootstrap_rate_distribution	bootstrap_rate_distribution
compare_shift_magnitudes	compare_shift_magnitudes
createSimulationTemplate	createSimulationTemplate
distribution-fit-data-frames	distribution-fit-data-frames
evaluateShiftRecovery	evaluateShiftRecovery
fisher_z_transform	fisher_z_transform
fit_rate_distribution	fit_rate_distribution
fit_regime_covariances	fit_regime_covariances
fit_regime_covariance_runs	fit_regime_covariance_runs
fit_waiting_time_distribution	fit_waiting_time_distribution
generateViridisColorScale	generateViridisColorScale
icTrajectory	icTrajectory
lineage_rates	lineage_rates
plot.icTrajectory	plot.icTrajectory
plot.rateMap	plot.rateMap
plot.rate_distribution_fit	plot.rate_distribution_fit
plot.regime_correlation_pca	plot.regime_correlation_pca
plot.regime_integration_relationships	plot.regime_integration_relationships
plot.regime_module_diagnostics	plot.regime_module_diagnostics
plot.shift_magnitude_comparison	plot.shift_magnitude_comparison
plot.shift_magnitude_comparison_set	plot.shift_magnitude_comparison_set
plot.shift_magnitude_counts	plot.shift_magnitude_counts
plot.shift_magnitude_count_set	plot.shift_magnitude_count_set
plot.shift_node_marks	shift_node_marks
print.bifrost_search	print.bifrost_search
print.bifrost_search_tuning_grid	print.bifrost_search_tuning_grid
print.bifrost_search_tuning_selection	print.bifrost_search_tuning_selection
print.bifrost_shift_recovery_evaluation	print.bifrost_shift_recovery_evaluation
print.bifrost_simulation_study	print.bifrost_simulation_study
print.bifrost_simulation_template	print.bifrost_simulation_template
print.rateMap	print.rateMap
rateMap	rateMap
rateMapControl	rateMapControl
rateMapRateFlags	rateMapRateFlags
rateMapView	rateMapView
regime_correlation_pca	regime_correlation_pca
regime_integration_pgls	regime_integration_pgls
regime_integration_relationships	regime_integration_relationships
regime_module_diagnostics	regime_module_diagnostics
runFalsePositiveSimulationStudy	runFalsePositiveSimulationStudy
runSearchTuningGrid	runSearchTuningGrid
runShiftRecoverySimulationStudy	runShiftRecoverySimulationStudy
searchOptimalConfiguration	searchOptimalConfiguration
selectTunedSearchParameters	selectTunedSearchParameters
shift_magnitude_counts	shift_magnitude_counts
shift_magnitude_groups	shift_magnitude_groups
shift_node_marks	shift_node_marks
shift_transitions	shift_transitions
shift_waiting_times	shift_waiting_times
simulateNullDataset	simulateNullDataset
simulateShiftedDataset	simulateShiftedDataset
summarize_regime_covariances	summarize_regime_covariances
summarize_regime_covariance_runs	summarize_regime_covariance_runs
