Files in bifrost

Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

R/lineage_rates.R R/shift-distributions.R R/simulation-generators.R R/searchOptimalConfiguration-helpers.R R/mvgls-starts.R R/simulation-template.R R/bifrost_search-methods.R R/formula-normalization.R R/simulation-tuning.R R/simulation-methods.R R/example-data.R R/regime-integration.R R/simulation-helpers.R R/rate-map-plot.R R/plotting-utils.R R/simulation-studies.R R/searchOptimalConfiguration.R R/icTrajectory.R R/utils.R R/rate-map.R

inst/CITATION

inst/WORDLIST

build/partial.rdb

tests/testthat.R tests/spelling.R tests/testthat/helper-example-data.R tests/testthat/test-shift-distributions.R tests/testthat/helper-search-characterization.R tests/testthat/test-runSearchTuningGrid.R tests/testthat/test-runFalsePositiveSimulationStudy.R tests/testthat/test-simulateNullDataset.R tests/testthat/helper-simulation-rng.R tests/testthat/test-recovery-f1.R tests/testthat/test-normalizeMvglsFormulaCall.R tests/testthat/helper-test-overrides.R tests/testthat/test-regime-integration.R tests/testthat/test-search-baseline-output.R tests/testthat/test-removeShiftFromTree.R tests/testthat/test-replicate-metrics.R tests/testthat/test-generatePaintedTrees.R tests/testthat/test-print-bifrost_simulation_template.R tests/testthat/test-simulation-covariance-helpers.R tests/testthat/test-paired-tuning-cache.R tests/testthat/test-formula-intercept.R tests/testthat/test-selectTunedSearchParameters.R tests/testthat/test-lineage_rates.R tests/testthat/test-getDescendants.R tests/testthat/test-tuning-fitting-settings.R tests/testthat/test-paintSubTree_removeShift.R tests/testthat/test-generateViridisColorScale.R tests/testthat/test-print-bifrost_simulation_study.R tests/testthat/test-icTrajectory.R tests/testthat/test-search-spinner.R tests/testthat/test-runShiftRecoverySimulationStudy.R tests/testthat/test-fitMvglsAndExtractIC.formula.R tests/testthat/test-whichShifts.R tests/testthat/test-vignette-html-widgets.R tests/testthat/test-search-progress.R tests/testthat/test-simulation-vignette-cache.R tests/testthat/test-createSimulationTemplate.R tests/testthat/test-compare-simulation-generators.R tests/testthat/test-paired-tuning-grid.R tests/testthat/test-print-bifrost_search.R tests/testthat/test-addShiftToModel.R tests/testthat/test-search-progress-silent.R tests/testthat/helper-avian-skeleton.R tests/testthat/test-search-progress-equivalence.R tests/testthat/test-search-background-history.R tests/testthat/test-extractRegimeVCVs.R tests/testthat/test-search-characterization.R tests/testthat/test-evaluateShiftRecovery.R tests/testthat/test-simulation-helpers.R tests/testthat/test-search-progress-atomic.R tests/testthat/test-simulation-formula-spec.R tests/testthat/test-covariance-validation-scale.R tests/testthat/test-search-progress-rng.R tests/testthat/test-mvgls-starts.R tests/testthat/test-searchOptimalConfiguration.R tests/testthat/helper-simulation-study-formula.R tests/testthat/test-paintSubTree_mod.R tests/testthat/test-serialized-artifacts.R tests/testthat/test-rate-map.R tests/testthat/test-simulateShiftedDataset.R tests/testthat/test-simulation-terminology.R tests/testthat/test-example-data.R tests/testthat/test-mvgls-functions.R tests/testthat/test-search-threading.R

tests/testthat/fixtures/mvgls-starts-historical.rds

tests/testthat/fixtures/search-characterization-baseline.rds

tests/testthat/fixtures/simdata.RDS

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

man/figures/logo.png

man/figures/schmidt-sciences-dark.png

bifrost documentation built on Nov. 5, 2026, 9:07 a.m.