R: Empirical Discovery of Differential Equations from Time Series Data

# Empirical Discovery of Differential Equations from Time Series Data

## Documentation for package ‘EmpiricalDynamics’ version 0.1.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

analysis_summary | Create Analysis Summary
analyze_bifurcations | Analyze Bifurcations
analyze_fixed_points | Analyze Fixed Points
annotate_hypotheses | Annotate Hypotheses
bootstrap_parameters | Bootstrap Confidence Intervals for Parameters
check_qualitative_behavior | Check Qualitative Behavior
coefficient_table | Generate Coefficient Table
compare_differentiation_methods | Compare Differentiation Methods
compare_estimation_methods | Compare OLS and GLS Estimation
compare_trajectories | Compare Simulated and Observed Trajectories
compute_derivative | Compute Derivative of a Time Series
compute_derivatives | Compute Derivatives for Specified Variables
compute_derivative_fd | Centered Finite Differences
compute_derivative_savgol | Savitzky-Golay Derivative
compute_derivative_spectral | Spectral (FFT) Differentiation
compute_derivative_spline | Smoothing Spline Derivative
compute_derivative_tvr | Total Variation Regularized Differentiation
compute_residuals | Compute Residuals from Symbolic Equation
construct_sde | Construct Stochastic Differential Equation Model
create_transformations | Create Candidate Transformations
cross_validate | Cross-Validate Discovered Equation
define_custom_operators | Define Custom Operators
diagnose_sampling_frequency | Diagnose Sampling Frequency
ed_theme | Default ggplot2 Theme for EmpiricalDynamics
estimate_diffusion_qv | Estimate Diffusion via Quadratic Variation
estimate_initial_values | Automatic Initial Value Estimation
estimate_sde_iterative | Iterative GLS Estimation for SDEs
exploration | Visual Exploration of Dynamical Structure
explore_dynamics | Comprehensive Dynamics Exploration
export_results | Export Results to Multiple Formats
fit_residual_distribution | Fit Residual Distribution
fit_specified_equation | Fit Specified Equation
format_equation | Format Equation for Display
generate_report | Generate Analysis Report
get_analysis_template | Get Analysis Template
get_pareto_set | Get Full Pareto Set
list_example_data | List Available Example Datasets
load_example_data | Load Example Dataset
model_comparison_table | Generate Model Comparison Table
model_conditional_variance | Model Conditional Variance
output | Output and Report Generation
parameterize_equation | Turn the Fitted Constants of a Discovered Equation into Free Parameters
plot.bifurcation_analysis | Plot Bifurcation Diagram
plot.cv_result | Plot CV Results
plot.trajectory_simulation | Plot Simulated Trajectories
plot.tvr_derivative | Plot Method for TVR Derivative
plot.validation_result | Plot Validation Results
plot_bivariate | Bivariate Scatter Plot
plot_pareto_front | Plot Pareto Front
plot_phase_1d | 1D Phase Diagram
plot_residual_diagnostics_panel | Plot Residual Diagnostics Panel
plot_surface_3d | 3D Response Surface
plot_timeseries | Time Series Plot
plot_trajectory_2d | 2D Trajectory Plot
plot_tvr_diagnostic | Diagnostic Plot for TVR Differentiation
predict.variance_model | Predict from Variance Model
preprocessing | Preprocessing Functions for Time Series Data
print.bifurcation_analysis | Print a Bifurcation Analysis
print.cv_result | Print CV Results
print.qualitative_check | Print Qualitative Check Results
print.residual_diagnostics | Print Residual Diagnostics
print.tvr_derivative | Print Method for TVR Derivative
print.validation_result | Print Validation Results
print_summary | Print Analysis Summary
read_empirical_data | Read Empirical Data from File
residual_analysis | Residual Analysis and Stochastic Differential Equations
residual_diagnostics | Comprehensive Residual Diagnostics
save_plots | Save Diagnostic Plots
select_equation | Select Equation from Pareto Front
select_lambda_cv_tvr | Cross-Validation Selection of Lambda for TVR
sensitivity_analysis | Parameter Sensitivity Analysis
setup_julia_backend | Setup Julia Backend
simulate_trajectory | Simulate Trajectory from SDE
specify_variables | Specify Variable Types for Dynamical Analysis
suggest_differentiation_method | Suggest Differentiation Method Based on Data Characteristics
symbolic_search | Symbolic Regression and Equation Discovery
symbolic_search_weighted | Weighted Symbolic Search
to_latex | Convert Equation to LaTeX
validate_model | Comprehensive Model Validation
validation | Validation of Discovered Equations