FluctuationAnalysisTools 1.10.0

Python library for DFA, Hurst exponent, and fluctuation analysis of time series.

FluctuationAnalysisTools

A Python library for creating and processing long-term dependent datasets, with a focus on statistical analysis tools for fluctuation analysis, time series generation, and signal processing.

Table of Contents

• Features
• Requirements
• Installation
• Quick Start
• Research and Examples
• Contributing
• License
• Citation

Features

• Synthetic Data Generation: Create datasets with controlled statistical properties (Hurst exponent, long-term dependencies) including:
  • Kasdin method for fractional Brownian noise (Kasdin, N. J. (1995). Discrete simulation of colored noise and stochastic processes and 1/f/sup /spl alpha// power law noise generation.).
  • FFT-based N-dimensional fractional Brownian motion (fBm) generator (Timmer, J., & Koenig, M. (1995). On generating power law noise).
• Fluctuation Analysis: Perform various fluctuation analysis methods including:
  • Detrended Fluctuation Analysis (DFA)
  • Detrended Partial Cross-Correlation Analysis (DPCCA)
  • Standard Fluctuation Analysis (FA)
  • SVD-based DFA
  • Multidimensional DFA
  • Quantitative Signal Analysis (QSS)
• Research Tools: Support scientific research in complex systems exhibiting long-range correlations
• Performance Optimized: Multi-threaded implementations with C++ extensions for large datasets

Requirements

• Python 3.8+
• NumPy
• SciPy
• Matplotlib (for visualization)
• C++ compiler (Mac and Windows packages contains precompiled binaries)

Installation

You can install FluctuationAnalysisTools from PyPI:

pip install FluctuationAnalysisTools

Or clone the repository and install locally:

git clone https://github.com/Digiratory/FluctuationAnalysisTools.git
cd StatTools
pip install .

Quick Start

You can find examples and published usages in the folder Research

If you used the project in your paper, you are welcome to ask us to add reference via a Pull Request or an Issue.

Generating Synthetic Data

from StatTools.generators import generate_fbn
import numpy as np

# Create a dataset with Hurst exponent H = 0.8 using the unified interface
hurst = 0.8
length = 1440

# Generate fractional Brownian noise using the default Kasdin method
fbn_series = generate_fbn(hurst=hurst, length=length)
print(f"Generated fBn series with shape: {fbn_series.shape}")

Analyzing Time Series

Detrended Fluctuation Analysis

from StatTools.generators import generate_fbn
from StatTools.analysis.dfa import dfa
from StatTools.analysis.utils import analyse_zero_cross_ff
import numpy as np

h = 0.7  # choose Hurst parameter
length = 6000  # vector's length

# Generate synthetic data using modern unified interface
trajectory = generate_fbn(hurst=h, length=length, method="kasdin").flatten()

# Analyze using functional-style DFA interface
s_vals, f2_vals = dfa(trajectory, degree=2)

# Calculate Hurst exponent from fluctuation function
f_vals = np.sqrt(f2_vals).reshape(1, -1)  # Convert F^2(s) to F(s) and reshape for analysis
s_vals_2d = s_vals.reshape(1, -1)  # Reshape scales to 2D array
hurst_result, _ = analyse_zero_cross_ff(f_vals, s_vals_2d)
hurst_exponent = hurst_result.slopes[0].value

print(f"Estimated H: {hurst_exponent:.3f} (Expected: {h:.3f})")

Support

For questions and discussions:

• GitHub Issues: https://github.com/Digiratory/FluctuationAnalysisTools/issues
• GitHub Discussions: https://github.com/Digiratory/FluctuationAnalysisTools/discussions

Research and Examples

Find comprehensive examples and published research in the research/ folder:

• Kalman Filter Examples
• LBFBM Generator Validation
• Video-based Analysis

If you've used StatTools in your research, consider contributing your examples via a Pull Request or Issue.

Contributing

We welcome contributions! Please see our Contributing Guide for details on:

• Setting up a development environment
• Code style and standards
• Testing guidelines
• Submitting pull requests

License

This project is licensed under the terms specified in LICENSE.txt.

Citation

If you use FluctuationAnalysisTools in your research, please cite:

@article{bogachev2023understanding,
  title={Understanding the complex interplay of persistent and antipersistent regimes in animal movement trajectories as a prominent characteristic of their behavioral pattern profiles: Towards an automated and robust model based quantification of anxiety test data},
  author={Bogachev, Mikhail I and Lyanova, Asya I and Sinitca, Aleksandr M and Pyko, Svetlana A and Pyko, Nikita S and Kuzmenko, Alexander V and Romanov, Sergey A and Brikova, Olga I and Tsygankova, Margarita and Ivkin, Dmitry Y and others},
  journal={Biomedical signal processing and control},
  volume={81},
  pages={104409},
  year={2023},
  publisher={Elsevier}
}

and

@article{bogachev2023video,
  title={Video-based marker-free tracking and multi-scale analysis of mouse locomotor activity and behavioral aspects in an open field arena: a perspective approach to the quantification of complex gait disturbances associated with Alzheimer's disease},
  author={Bogachev, Mikhail and Sinitca, Aleksandr and Grigarevichius, Konstantin and Pyko, Nikita and Lyanova, Asya and Tsygankova, Margarita and Davletshin, Eldar and Petrov, Konstantin and Ageeva, Tatyana and Pyko, Svetlana and others},
  journal={Frontiers in Neuroinformatics},
  volume={17},
  pages={1101112},
  year={2023},
  publisher={Frontiers Media SA}
}

Changelog

See CHANGELOG.md for version history and updates.