API Reference

Core Functions

Model Fitting

• fit: Main function for fitting models to data
• fit_parallel: Parallel version of fit for large datasets
• fit_hierarchical: Hierarchical model fitting

Data Analysis

• analyze_results: Analyze fitting results
• plot_results: Plot fitting results
• save_results: Save results to disk

Data Types

• RNAData: RNA count data structure
• TraceData: Live cell imaging data structure
• DwellTimeData: Dwell time data structure

Model Types

• HMMReporter: Hidden Markov model for reporter data
• GMmodel: Gene model structure
• Transformation: Data transformation structure

Traits

• HierarchicalTrait: Hierarchical model trait
• GridTrait: Grid search trait
• CouplingTrait: Coupled model trait

Utility Functions

Data Management

• rna_setup: Set up project directory structure
• load_data: Load data from files
• save_data: Save data to files

Model Management

• create_model: Create a new model instance
• register_model: Register a model type
• print_model: Print model details

Analysis Tools

• calculate_statistics: Calculate basic statistics
• generate_plots: Generate standard plots
• export_results: Export results to various formats

Advanced Features

Parallel Processing

• setup_parallel: Set up parallel processing
• cleanup_parallel: Clean up parallel resources

Bayesian Analysis

• bayesian_fit: Bayesian model fitting
• mcmc_analysis: MCMC analysis tools

Model Validation

• validate_model: Validate model assumptions
• cross_validate: Cross-validation tools