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  "Title": "Branch-Level Inference Framework for Recognizing Optimal Shifts\nin Traits",
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  "Authors@R": "c(\nperson(given = c(\"Jacob\", \"S.\"), family = \"Berv\", email = \"jacob.berv@gmail.com\", role = c(\"aut\", \"cre\", \"cph\", \"fnd\"), comment = c(ORCID = \"0000-0002-5962-0621\")),\nperson(given = \"Nathan\", family = \"Fox\", role = \"aut\", comment = c(ORCID = \"0000-0002-2816-9751\")),\nperson(given = c(\"Matt\", \"J.\"), family = \"Thorstensen\", role = \"aut\", comment = c(ORCID = \"0000-0002-7870-3369\")),\nperson(given = \"Henry\", family = \"Lloyd-Laney\", role = \"aut\", comment = c(ORCID = \"0000-0003-4650-8937\")),\nperson(given = c(\"Emily\", \"M.\"), family = \"Troyer\", role = \"aut\", comment = c(ORCID = \"0000-0001-7478-2306\")),\nperson(given = c(\"Rafael\", \"A.\"), family = \"Rivero-Vega\", role = \"aut\", comment = c(ORCID = \"0000-0001-5937-6377\")),\nperson(given = c(\"Stephen\", \"A.\"), family = \"Smith\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0003-2035-9531\")),\nperson(given = \"Matt\", family = \"Friedman\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0002-0114-7384\")),\nperson(given = c(\"David\", \"F.\"), family = \"Fouhey\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0001-5028-5161\")),\nperson(given = c(\"Brian\", \"C.\"), family = \"Weeks\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0003-2967-2970\")))",
  "Description": "Methods for detecting, visualizing, and evaluating\ncladogenic shifts in multivariate trait data on phylogenies.\nImplements penalized-likelihood multivariate generalized least\nsquares models and a greedy step-wise shift search for\nhigh-dimensional trait datasets and large trees via\nsearchOptimalConfiguration(). Provides tools for inspecting\nsearch trajectories, summarizing branch and lineage rates,\nanalyzing shift timing and magnitudes, estimating post-hoc\nregime covariance and integration, and running simulation-based\ncalibration and tuning. The search follows approaches developed\nin Smith et al. (2023) <doi:10.1111/nph.19099> and Berv et al.\n(2024) <doi:10.1126/sciadv.adp0114>. Methods build on\nmultivariate generalized least squares approaches described in\nClavel et al. (2019) <doi:10.1093/sysbio/syy045> and\nimplemented in the mvgls() function from the 'mvMORPH' package.\nDocumentation and worked examples are available at\n<https://jakeberv.com/bifrost/>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
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  "Date/Publication": "2026-10-28 22:40:55 UTC",
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  "Author": "Jacob S. Berv [aut, cre, cph, fnd] (ORCID:\n<https://orcid.org/0000-0002-5962-0621>),\nNathan Fox [aut] (ORCID: <https://orcid.org/0000-0002-2816-9751>),\nMatt J. Thorstensen [aut] (ORCID:\n<https://orcid.org/0000-0002-7870-3369>),\nHenry Lloyd-Laney [aut] (ORCID:\n<https://orcid.org/0000-0003-4650-8937>),\nEmily M. Troyer [aut] (ORCID: <https://orcid.org/0000-0001-7478-2306>),\nRafael A. Rivero-Vega [aut] (ORCID:\n<https://orcid.org/0000-0001-5937-6377>),\nStephen A. Smith [aut, fnd] (ORCID:\n<https://orcid.org/0000-0003-2035-9531>),\nMatt Friedman [aut, fnd] (ORCID:\n<https://orcid.org/0000-0002-0114-7384>),\nDavid F. Fouhey [aut, fnd] (ORCID:\n<https://orcid.org/0000-0001-5028-5161>),\nBrian C. Weeks [aut, fnd] (ORCID:\n<https://orcid.org/0000-0003-2967-2970>)",
  "Maintainer": "Jacob S. Berv <jacob.berv@gmail.com>",
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    "createSimulationTemplate",
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    "fit_rate_distribution",
    "fit_regime_covariance_runs",
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    "generateViridisColorScale",
    "icTrajectory",
    "lineage_rates",
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    "rateMapRateFlags",
    "rateMapView",
    "regime_correlation_pca",
    "regime_integration_pgls",
    "regime_integration_relationships",
    "regime_module_diagnostics",
    "runFalsePositiveSimulationStudy",
    "runSearchTuningGrid",
    "runShiftRecoverySimulationStudy",
    "searchOptimalConfiguration",
    "selectTunedSearchParameters",
    "shift_magnitude_counts",
    "shift_magnitude_groups",
    "shift_node_marks",
    "shift_transitions",
    "shift_waiting_times",
    "simulateNullDataset",
    "simulateShiftedDataset",
    "summarize_regime_covariance_runs",
    "summarize_regime_covariances"
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      "title": "Convert a fixed-IC search tuning grid to a data frame",
      "topics": [
        "as.data.frame.bifrost_search_tuning_grid"
      ]
    },
    {
      "page": "as.data.frame.bifrost_search_tuning_selection",
      "title": "Convert a tuned search-parameter selection to a data frame",
      "topics": [
        "as.data.frame.bifrost_search_tuning_selection"
      ]
    },
    {
      "page": "as.data.frame.bifrost_shift_recovery_evaluation",
      "title": "Convert a shift-recovery evaluation to a data frame",
      "topics": [
        "as.data.frame.bifrost_shift_recovery_evaluation"
      ]
    },
    {
      "page": "as.data.frame.bifrost_simulation_study",
      "title": "Convert a bifrost simulation study to a data frame",
      "topics": [
        "as.data.frame.bifrost_simulation_study"
      ]
    },
    {
      "page": "as.data.frame.regime_correlation_pca",
      "title": "Convert Regime Correlation PCA Results to Data Frames",
      "topics": [
        "as.data.frame.regime_correlation_pca"
      ]
    },
    {
      "page": "as.data.frame.regime_integration_relationships",
      "title": "Convert Regime Integration Relationship Results to Data Frames",
      "topics": [
        "as.data.frame.regime_integration_relationships"
      ]
    },
    {
      "page": "as.data.frame.regime_module_diagnostics",
      "title": "Convert Regime Module Diagnostics to Data Frames",
      "topics": [
        "as.data.frame.regime_module_diagnostics"
      ]
    },
    {
      "page": "bifrost_example_file",
      "title": "Locate a verified empirical example-data artifact",
      "topics": [
        "bifrost_example_file"
      ]
    },
    {
      "page": "bootstrap_rate_distribution",
      "title": "Bootstrap A Fitted Rate Distribution",
      "topics": [
        "bootstrap_rate_distribution"
      ]
    },
    {
      "page": "compare_shift_magnitudes",
      "title": "Compare Rate-Shift Magnitudes",
      "topics": [
        "compare_shift_magnitudes"
      ]
    },
    {
      "page": "createSimulationTemplate",
      "title": "Create an Empirically Calibrated Simulation Template for 'bifrost'",
      "topics": [
        "createSimulationTemplate"
      ]
    },
    {
      "page": "distribution-fit-data-frames",
      "title": "Coerce Shift And Distribution Summaries To Data Frames",
      "topics": [
        "as.data.frame.rate_distribution_fit",
        "as.data.frame.shift_magnitude_comparison",
        "as.data.frame.shift_magnitude_comparison_set",
        "as.data.frame.shift_magnitude_counts",
        "as.data.frame.shift_magnitude_count_set",
        "as.data.frame.waiting_time_distribution_fit",
        "distribution-fit-data-frames"
      ]
    },
    {
      "page": "evaluateShiftRecovery",
      "title": "Evaluate Shift Recovery Against Simulated Ground Truth",
      "topics": [
        "evaluateShiftRecovery"
      ]
    },
    {
      "page": "fisher_z_transform",
      "title": "Fisher's Z Transformation",
      "topics": [
        "fisher_z_transform"
      ]
    },
    {
      "page": "fit_rate_distribution",
      "title": "Fit Candidate Distributions To Rates",
      "topics": [
        "fit_rate_distribution"
      ]
    },
    {
      "page": "fit_regime_covariance_runs",
      "title": "Fit Post-hoc Regime Covariance Models Across Runs",
      "topics": [
        "fit_regime_covariance_runs"
      ]
    },
    {
      "page": "fit_regime_covariances",
      "title": "Fit Independent Post-hoc Regime Covariance Models",
      "topics": [
        "fit_regime_covariances"
      ]
    },
    {
      "page": "fit_waiting_time_distribution",
      "title": "Fit Candidate Distributions To Shift Waiting Times",
      "topics": [
        "fit_waiting_time_distribution"
      ]
    },
    {
      "page": "generateViridisColorScale",
      "title": "Generate Viridis Color Palette for Ranked Parameters",
      "topics": [
        "generateViridisColorScale"
      ]
    },
    {
      "page": "icTrajectory",
      "title": "Create an Information-Criterion Trajectory",
      "topics": [
        "icTrajectory"
      ]
    },
    {
      "page": "lineage_rates",
      "title": "Compute Weighted Lineage Rates",
      "topics": [
        "lineage_rates"
      ]
    },
    {
      "page": "plot.icTrajectory",
      "title": "Plot an Information-Criterion Trajectory",
      "topics": [
        "plot.icTrajectory"
      ]
    },
    {
      "page": "plot.rate_distribution_fit",
      "title": "Plot A Fitted Rate Distribution",
      "topics": [
        "plot.rate_distribution_fit"
      ]
    },
    {
      "page": "plot.rateMap",
      "title": "Plot 'rateMap' Objects",
      "topics": [
        "plot.rateMap"
      ]
    },
    {
      "page": "plot.regime_correlation_pca",
      "title": "Plot Regime Correlation PCA Results",
      "topics": [
        "plot.regime_correlation_pca"
      ]
    },
    {
      "page": "plot.regime_integration_relationships",
      "title": "Plot Regime Rate-Integration Relationships",
      "topics": [
        "plot.regime_integration_relationships"
      ]
    },
    {
      "page": "plot.regime_module_diagnostics",
      "title": "Plot Regime Module Diagnostics",
      "topics": [
        "plot.regime_module_diagnostics"
      ]
    },
    {
      "page": "plot.shift_magnitude_comparison",
      "title": "Plot One Shift-Magnitude Comparison",
      "topics": [
        "plot.shift_magnitude_comparison"
      ]
    },
    {
      "page": "plot.shift_magnitude_comparison_set",
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