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  "Package": "EmpiricalDynamics",
  "Title": "Empirical Discovery of Differential Equations from Time Series\nData",
  "Version": "0.1.14",
  "Authors@R": "person(\"José Mauricio\", \"Gómez Julián\", email = \"isadore.nabi@pm.me\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-2412-3150\"))",
  "Description": "A comprehensive toolkit for discovering differential and\ndifference equations from empirical time series data using\nsymbolic regression. The package implements a complete workflow\nfrom data preprocessing (including Total Variation Regularized\ndifferentiation for noisy economic data), visual exploration of\ndynamical structure, and symbolic equation discovery via\ngenetic algorithms. It leverages a high-performance 'Julia'\nbackend ('SymbolicRegression.jl') to provide industrial-grade\nrobustness, physics-informed constraints, and rigorous\nout-of-sample validation. Designed for economists, physicists,\nand researchers studying dynamical systems from observational\ndata.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "SystemRequirements": "Julia (>= 1.6)",
  "Config/testthat/edition": "3",
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  "URL": "https://github.com/IsadoreNabi/EmpiricalDynamics",
  "BugReports": "https://github.com/IsadoreNabi/EmpiricalDynamics/issues",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-26 09:58:02 UTC",
    "User": "root"
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  "Author": "José Mauricio Gómez Julián [aut, cre]\n(<https://orcid.org/0009-0000-2412-3150>)",
  "Maintainer": "José Mauricio Gómez Julián <isadore.nabi@pm.me>",
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  "Repository": "https://isadorenabi.r-universe.dev",
  "Date/Publication": "2026-08-27 19:07:51 UTC",
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  "_created": "2026-09-26T09:58:02.000Z",
  "_published": "2026-09-26T10:02:35.924Z",
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    "author": "José Mauricio Gómez Julián <isadore.nabi@pm.me>",
    "committer": "José Mauricio Gómez Julián <isadore.nabi@pm.me>",
    "message": "Refuse an unrecognised expected_feature instead of dropping it, and grow bounded and monotonicity; bump to 0.1.14\n\ncheck_qualitative_behavior() honoured exactly two names of expected_features\nand dropped every other one in silence, while its own documentation promised\nfour. A call asking for bounded = TRUE returned 0/0 checks passed: a call that\nlooks like a corroboration and corroborates nothing. The same silence covered\nevery typo -- stability_patern lowered the count of checks without saying which\none went missing -- and access was by $, whose partial matching honoured\nn_fixed_points_max as n_fixed_points.\n\nThe vocabulary is now closed and matched exactly, values are validated, and the\nnumber of checks equals the number of features requested, asserted before\nreturning. validate_model() validates the same list first thing, and its\nqualitative stage no longer swallows the refusal.\n\nbounded is decided by algebra rather than by a horizon: the field points inward\nat both ends of the observed range, so the range is invariant. It is read over\nthe observed range unwidened -- on the widened range the textbook logistic\nanswers FALSE -- and it claims range invariance, which is strictly stronger\nthan global boundedness. monotonicity is the sign of the field over the same\nrange. Both are read from the field ed_field_of() builds, the one\nanalyze_fixed_points() finds its roots with, so there is no second evaluator to\ndrift from the first.\n\nTwo checks that used to vanish are back in the tally: an expected\nstability_pattern with no fixed point found, and data without the variable,\nwhich fell back on a range nobody measured.\n",
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    "analyze_bifurcations",
    "analyze_fixed_points",
    "annotate_hypotheses",
    "bootstrap_parameters",
    "check_qualitative_behavior",
    "coefficient_table",
    "compare_differentiation_methods",
    "compare_estimation_methods",
    "compare_trajectories",
    "compute_derivative",
    "compute_derivative_fd",
    "compute_derivative_savgol",
    "compute_derivative_spectral",
    "compute_derivative_spline",
    "compute_derivative_tvr",
    "compute_derivatives",
    "compute_residuals",
    "construct_sde",
    "create_transformations",
    "cross_validate",
    "define_custom_operators",
    "diagnose_sampling_frequency",
    "ed_consensus_fixed_points",
    "ed_derivative_step",
    "ed_theme",
    "estimate_diffusion_qv",
    "estimate_initial_values",
    "estimate_sde_iterative",
    "explore_dynamics",
    "export_results",
    "fit_residual_distribution",
    "fit_specified_equation",
    "format_equation",
    "generate_report",
    "get_analysis_template",
    "get_pareto_set",
    "list_example_data",
    "load_example_data",
    "model_comparison_table",
    "model_conditional_variance",
    "parameterize_equation",
    "plot_bivariate",
    "plot_pareto_front",
    "plot_phase_1d",
    "plot_residual_diagnostics_panel",
    "plot_surface_3d",
    "plot_timeseries",
    "plot_trajectory_2d",
    "plot_tvr_diagnostic",
    "print_summary",
    "read_empirical_data",
    "residual_diagnostics",
    "save_plots",
    "select_equation",
    "select_lambda_cv_tvr",
    "sensitivity_analysis",
    "setup_julia_backend",
    "simulate_trajectory",
    "specify_variables",
    "suggest_differentiation_method",
    "symbolic_search",
    "symbolic_search_weighted",
    "to_latex",
    "validate_model"
  ],
  "_help": [
    {
      "page": "analysis_summary",
      "title": "Create Analysis Summary",
      "topics": [
        "analysis_summary"
      ]
    },
    {
      "page": "analyze_bifurcations",
      "title": "Analyze Bifurcations",
      "topics": [
        "analyze_bifurcations"
      ]
    },
    {
      "page": "analyze_fixed_points",
      "title": "Analyze Fixed Points",
      "topics": [
        "analyze_fixed_points"
      ]
    },
    {
      "page": "annotate_hypotheses",
      "title": "Annotate Hypotheses",
      "topics": [
        "annotate_hypotheses"
      ]
    },
    {
      "page": "bootstrap_parameters",
      "title": "Bootstrap Confidence Intervals for Parameters",
      "topics": [
        "bootstrap_parameters"
      ]
    },
    {
      "page": "check_qualitative_behavior",
      "title": "Check Qualitative Behavior",
      "topics": [
        "check_qualitative_behavior"
      ]
    },
    {
      "page": "coefficient_table",
      "title": "Generate Coefficient Table",
      "topics": [
        "coefficient_table"
      ]
    },
    {
      "page": "compare_differentiation_methods",
      "title": "Compare Differentiation Methods",
      "topics": [
        "compare_differentiation_methods"
      ]
    },
    {
      "page": "compare_estimation_methods",
      "title": "Compare OLS and GLS Estimation",
      "topics": [
        "compare_estimation_methods"
      ]
    },
    {
      "page": "compare_trajectories",
      "title": "Compare Simulated and Observed Trajectories",
      "topics": [
        "compare_trajectories"
      ]
    },
    {
      "page": "compute_derivative",
      "title": "Compute Derivative of a Time Series",
      "topics": [
        "compute_derivative"
      ]
    },
    {
      "page": "compute_derivative_fd",
      "title": "Centered Finite Differences",
      "topics": [
        "compute_derivative_fd"
      ]
    },
    {
      "page": "compute_derivative_savgol",
      "title": "Savitzky-Golay Derivative",
      "topics": [
        "compute_derivative_savgol"
      ]
    },
    {
      "page": "compute_derivative_spectral",
      "title": "Spectral (FFT) Differentiation",
      "topics": [
        "compute_derivative_spectral"
      ]
    },
    {
      "page": "compute_derivative_spline",
      "title": "Smoothing Spline Derivative",
      "topics": [
        "compute_derivative_spline"
      ]
    },
    {
      "page": "compute_derivative_tvr",
      "title": "Total Variation Regularized Differentiation",
      "topics": [
        "compute_derivative_tvr"
      ]
    },
    {
      "page": "compute_derivatives",
      "title": "Compute Derivatives for Specified Variables",
      "topics": [
        "compute_derivatives"
      ]
    },
    {
      "page": "compute_residuals",
      "title": "Compute Residuals from Symbolic Equation",
      "topics": [
        "compute_residuals"
      ]
    },
    {
      "page": "construct_sde",
      "title": "Construct Stochastic Differential Equation Model",
      "topics": [
        "construct_sde"
      ]
    },
    {
      "page": "create_transformations",
      "title": "Create Candidate Transformations",
      "topics": [
        "create_transformations"
      ]
    },
    {
      "page": "cross_validate",
      "title": "Cross-Validate Discovered Equation",
      "topics": [
        "cross_validate"
      ]
    },
    {
      "page": "define_custom_operators",
      "title": "Define Custom Operators",
      "topics": [
        "define_custom_operators"
      ]
    },
    {
      "page": "diagnose_sampling_frequency",
      "title": "Diagnose Sampling Frequency",
      "topics": [
        "diagnose_sampling_frequency"
      ]
    },
    {
      "page": "ed_consensus_fixed_points",
      "title": "Reduce a Posterior of Fixed Points to Branches",
      "topics": [
        "ed_consensus_fixed_points"
      ]
    },
    {
      "page": "ed_derivative_step",
      "title": "The step of the central difference this package differentiates with",
      "topics": [
        "ed_derivative_step"
      ]
    },
    {
      "page": "ed_theme",
      "title": "Default ggplot2 Theme for EmpiricalDynamics",
      "topics": [
        "ed_theme"
      ]
    },
    {
      "page": "estimate_diffusion_qv",
      "title": "Estimate Diffusion via Quadratic Variation",
      "topics": [
        "estimate_diffusion_qv"
      ]
    },
    {
      "page": "estimate_initial_values",
      "title": "Automatic Initial Value Estimation",
      "topics": [
        "estimate_initial_values"
      ]
    },
    {
      "page": "estimate_sde_iterative",
      "title": "Iterative GLS Estimation for SDEs",
      "topics": [
        "estimate_sde_iterative"
      ]
    },
    {
      "page": "exploration",
      "title": "Visual Exploration of Dynamical Structure",
      "topics": [
        "exploration"
      ]
    },
    {
      "page": "explore_dynamics",
      "title": "Comprehensive Dynamics Exploration",
      "topics": [
        "explore_dynamics"
      ]
    },
    {
      "page": "export_results",
      "title": "Export Results to Multiple Formats",
      "topics": [
        "export_results"
      ]
    },
    {
      "page": "fit_residual_distribution",
      "title": "Fit Residual Distribution",
      "topics": [
        "fit_residual_distribution"
      ]
    },
    {
      "page": "fit_specified_equation",
      "title": "Fit Specified Equation",
      "topics": [
        "fit_specified_equation"
      ]
    },
    {
      "page": "format_equation",
      "title": "Format Equation for Display",
      "topics": [
        "format_equation"
      ]
    },
    {
      "page": "generate_report",
      "title": "Generate Analysis Report",
      "topics": [
        "generate_report"
      ]
    },
    {
      "page": "get_analysis_template",
      "title": "Get Analysis Template",
      "topics": [
        "get_analysis_template"
      ]
    },
    {
      "page": "get_pareto_set",
      "title": "Get Full Pareto Set",
      "topics": [
        "get_pareto_set"
      ]
    },
    {
      "page": "list_example_data",
      "title": "List Available Example Datasets",
      "topics": [
        "list_example_data"
      ]
    },
    {
      "page": "load_example_data",
      "title": "Load Example Dataset",
      "topics": [
        "load_example_data"
      ]
    },
    {
      "page": "model_comparison_table",
      "title": "Generate Model Comparison Table",
      "topics": [
        "model_comparison_table"
      ]
    },
    {
      "page": "model_conditional_variance",
      "title": "Model Conditional Variance",
      "topics": [
        "model_conditional_variance"
      ]
    },
    {
      "page": "output",
      "title": "Output and Report Generation",
      "topics": [
        "output"
      ]
    },
    {
      "page": "parameterize_equation",
      "title": "Turn the Fitted Constants of a Discovered Equation into Free Parameters",
      "topics": [
        "parameterize_equation"
      ]
    },
    {
      "page": "plot_bivariate",
      "title": "Bivariate Scatter Plot",
      "topics": [
        "plot_bivariate"
      ]
    },
    {
      "page": "plot_pareto_front",
      "title": "Plot Pareto Front",
      "topics": [
        "plot_pareto_front"
      ]
    },
    {
      "page": "plot_phase_1d",
      "title": "1D Phase Diagram",
      "topics": [
        "plot_phase_1d"
      ]
    },
    {
      "page": "plot_residual_diagnostics_panel",
      "title": "Plot Residual Diagnostics Panel",
      "topics": [
        "plot_residual_diagnostics_panel"
      ]
    },
    {
      "page": "plot_surface_3d",
      "title": "3D Response Surface",
      "topics": [
        "plot_surface_3d"
      ]
    },
    {
      "page": "plot_timeseries",
      "title": "Time Series Plot",
      "topics": [
        "plot_timeseries"
      ]
    },
    {
      "page": "plot_trajectory_2d",
      "title": "2D Trajectory Plot",
      "topics": [
        "plot_trajectory_2d"
      ]
    },
    {
      "page": "plot_tvr_diagnostic",
      "title": "Diagnostic Plot for TVR Differentiation",
      "topics": [
        "plot_tvr_diagnostic"
      ]
    },
    {
      "page": "plot.bifurcation_analysis",
      "title": "Plot Bifurcation Diagram",
      "topics": [
        "plot.bifurcation_analysis"
      ]
    },
    {
      "page": "plot.cv_result",
      "title": "Plot CV Results",
      "topics": [
        "plot.cv_result"
      ]
    },
    {
      "page": "plot.trajectory_simulation",
      "title": "Plot Simulated Trajectories",
      "topics": [
        "plot.trajectory_simulation"
      ]
    },
    {
      "page": "plot.tvr_derivative",
      "title": "Plot Method for TVR Derivative",
      "topics": [
        "plot.tvr_derivative"
      ]
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      "title": "Getting Started with EmpiricalDynamics",
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      "headings": [
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        "Installation",
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        "Step 1: Load Data and Compute Derivatives",
        "Step 2: Explore the Data",
        "Step 3: Fit the Equation",
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      "modified": "2026-01-21 16:42:45",
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