HyGCS

User Guide

  • Installation
    • Requirements
      • Python Version
      • Dependencies
    • Installation from Source
    • Alternative: Install Dependencies Only
    • Verify Installation
    • Troubleshooting
      • Import Errors
      • Missing Dependencies
      • Jupyter Notebook Issues
    • Next Steps
  • Quick Start Guide
    • Import the Package
    • Single Event Hysteresis Analysis
      • Load Your Data
      • Calculate Hysteresis Metrics
      • Extract Results
      • Visualize Individual Methods
    • Time Series Classification
      • Prepare Your Data
      • Optional: High-Resolution Flow Data
      • Run Classification
      • Examine Results
      • Visualize Phase Sequence
      • Create Diagnostic Plots
      • Create Hysteresis Plots
    • CVc/CVq Variability Analysis
      • Compute Rolling Windows
      • Interpret Results
    • C-Q Slope Calculation
    • Understanding the Output
      • Hysteresis Metrics
      • Geochemical Phases
      • Confidence Scores
    • Common Workflows
      • Compare Multiple Events
      • Multi-Site Summary Statistics
      • Multi-Compound Comparison
    • Best Practices
    • Troubleshooting
      • “Not enough data points”
      • “All NaN results”
      • “Classification seems wrong”
    • Next Steps
  • Examples
    • Available Notebooks
      • demo_gcs_core_function.ipynb
      • test_gcs.ipynb
    • Running the Notebooks
      • Install Jupyter
      • Launch Jupyter
      • Interactive Execution
    • Example Workflows
      • Workflow 1: Analyze Single Storm Event
      • Workflow 2: Multi-Site Classification
      • Workflow 3: Multi-Compound Comparison
      • Workflow 4: CVc/CVq Analysis
    • Expected Outputs
      • From demo_gcs_core_function.ipynb
      • From test_gcs.ipynb
    • Troubleshooting
      • Notebook Won’t Open
      • Plots Don’t Display
      • Module Import Errors
      • Missing Data Files
    • Further Resources
    • Next Steps
  • Scientific Background
    • Hysteresis in C-Q Relationships
      • Direction and Interpretation
    • Implemented Hysteresis Methods
      • HARP Method (Roberts et al., 2023)
      • Zuecco Index (Zuecco et al., 2016)
      • Lloyd/Lawler Methods (2016, 2006)
    • CVc/CVq Framework
      • Coefficient of Variation Approach (Musolff et al., 2015)
    • C-Q Relationships
      • Power-Law Model (Thompson et al., 2011)
    • Geochemical Phase Classification
      • The 6 Phases
      • Percentile-Based Thresholds
      • Window-Scale Hysteresis
      • Hierarchical Rule System
    • Critical Perspective
      • Knapp & Musolff (2024) - Critical Assessment
    • Best Practices
    • See Also

API Reference

  • Core Analysis Functions
    • Hysteresis Metrics
      • calculate_all_hysteresis_metrics()
    • CVc/CVq Variability Analysis
      • compute_cvc_cvq_windows()
    • C-Q Slope Calculation
      • compute_cq_slope()
    • Flow Dynamics Analysis
      • analyze_segment_flow_dynamics()
    • Statistical Functions
      • compute_change_percentiles()
    • Notes
    • See Also
  • Classification Functions
    • Main Classification Function
      • classify_geochemical_phase()
    • Segment Classification
      • classify_segment_phase()
    • Simple C-Q Classification
      • classify_cq_behavior_simple()
    • Classification Logic
    • Scientific Basis
    • Usage Examples
    • See Also
  • Visualization Functions
    • Phase Visualization
      • create_phase_sequence_plot()
      • create_diagnostic_plot()
    • Hysteresis Visualization
      • create_hysteresis_plot()
      • create_multi_compound_hysteresis_plot()
      • create_hysteresis_timeline()
    • Summary Statistics
      • create_hysteresis_summary_stats()
    • Style and Color Functions
      • get_line_style_from_hi_class()
      • calculate_log_thickness()
    • Color Schemes
      • phase_colors
      • phase_names
      • hyphase_colors
    • Usage Examples
    • Customization
    • Notes
    • See Also
  • Hysteresis Methods
    • HARP Method
      • calculate_harp_metrics()
      • harp_plot()
    • Zuecco Method
      • calculate_zuecco_metrics()
      • zuecco_plot()
    • Lloyd/Lawler Methods
      • calculate_lawlerlloyd_metrics()
      • lloyd_plot()
    • Comparison and Selection
      • When to Use Each Method
      • Convergent Evidence
    • Usage Example
    • Data Requirements
    • See Also

Additional Information

  • License
    • Summary
    • Full License Text
    • Attribution Requirements
    • Adapted Works
    • Disclaimer
    • Copyright
    • Contact
  • Citation
    • Software Citation
      • BibTeX
      • Text
    • Methodology Papers
      • HARP Method
      • Zuecco Index
      • Lloyd/Lawler Methods
      • CVc/CVq Framework
      • C-Q Relationships
      • Critical Perspective
    • Example Publication Text
      • Methods Section
      • Results Section
      • Acknowledgments Section
    • Related Publications
    • Data Availability Statement
    • Acknowledgments
  • Changelog
    • Version 0.5 (December 2025)
      • Package Organization
      • Function Changes
      • Bug Fixes
      • Visualization Improvements
      • Documentation
      • Testing
      • GitHub Readiness
    • Version 4.0 (Previous)
      • Known Issues in v4.0
    • Migration from v4.0 to v0.5
      • Breaking Changes
      • Deprecated Features
    • Future Plans
      • Version 0.6 (Planned)
      • Version 1.0 (Planned)
    • Reporting Issues
    • Contributing
    • Version Numbering
HyGCS
  • Index

Index

A | C | G | H | L | P | Z

A

  • analyze_segment_flow_dynamics() (in module hygcs.gcs_core)

C

  • calculate_all_hysteresis_metrics() (in module hygcs.gcs_core)
  • calculate_harp_metrics() (in module hygcs.harp)
  • calculate_lawlerlloyd_metrics() (in module hygcs.lloyd)
  • calculate_log_thickness() (in module hygcs.gcs_visualization)
  • calculate_zuecco_metrics() (in module hygcs.zuecco)
  • classify_cq_behavior_simple() (in module hygcs.gcs_classification)
  • classify_geochemical_phase() (in module hygcs.gcs_classification)
  • classify_segment_phase() (in module hygcs.gcs_classification)
  • compute_change_percentiles() (in module hygcs.gcs_core)
  • compute_cq_slope() (in module hygcs.gcs_core)
  • compute_cvc_cvq_windows() (in module hygcs.gcs_core)
  • create_diagnostic_plot() (in module hygcs.gcs_visualization)
  • create_hysteresis_plot() (in module hygcs.gcs_visualization)
  • create_hysteresis_summary_stats() (in module hygcs.gcs_visualization)
  • create_hysteresis_timeline() (in module hygcs.gcs_visualization)
  • create_multi_compound_hysteresis_plot() (in module hygcs.gcs_visualization)
  • create_phase_sequence_plot() (in module hygcs.gcs_visualization)

G

  • get_line_style_from_hi_class() (in module hygcs.gcs_visualization)

H

  • harp_plot() (in module hygcs.harp)
  • hyphase_colors (in module hygcs.gcs_visualization)

L

  • lloyd_plot() (in module hygcs.lloyd)

P

  • phase_colors (in module hygcs.gcs_visualization)
  • phase_names (in module hygcs.gcs_visualization)

Z

  • zuecco_plot() (in module hygcs.zuecco)

© Copyright 2025, Conrad Jackisch, Anita Sanchez.

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