rqa-analysis 1.0.1

Fast Recurrence Quantification Analysis (RQA) with a high-performance C++ core

Recurrence Quantification Analysis (RQA) Python & C++ Package

This package provides fast and flexible tools for performing Auto Recurrence Quantification Analysis (autoRQA), Cross Recurrence Quantification Analysis (crossRQA), Multivariate Recurrence Quantification Analysis (multivariateRQA), and Diagonal Recurrence Profiles (DRP) on time series data. It supports phase space reconstruction, recurrence plot generation, and computation of standard RQA metrics, including %REC, %DET, MaxLine, MeanLine, Entropy, Laminarity, Trapping Time, and more.

Key Features

• High-performance C++ core with Python interface for speed
• Four analysis modes:
  • Traditional RQA: Single time series with time-delay embedding
  • Cross-RQA: Compare two time series or systems
  • Multivariate RQA: Direct analysis of multi-dimensional systems
  • Diagonal Recurrence Profile: Compute recurrence across a range of time lags
• Comprehensive metrics: All standard RQA measures plus vertical line statistics
• Visualization tools: Recurrence plots with optional time series overlay
• Example datasets: Real physiological data, chaotic systems, and synthetic data
• Robust error handling: Graceful handling of short time series and edge cases

Installation

From PyPI (recommended)

pip install rqa-analysis

From source

git clone https://github.com/xkiwilabs/Recurrence-Quantification-Analysis.git
cd Recurrence-Quantification-Analysis
pip install .

Building from source requires a C++ compiler (C++14). See INSTALL.md for detailed OS-specific instructions and troubleshooting.

Parameters

The following parameters are used for running Auto RQA (autoRQA), Cross RQA (crossRQA), Multivariate RQA (multivariateRQA) and computing Diagonal Recurrence Profiles (DRP). Note that multivariate RQA does not require embedding parameters (eDim, tLag) as it uses the actual system dimensions directly.

Parameter List

Parameter	Type	Default	Description
norm	int/str	1	Normalization method for input time series data:
			- 0: No normalization (leave data as-is).
			- 1: Normalize to the unit interval [0, 1].
			- 2 or 'zscore': Standardize using Z-score normalization (mean = 0, std = 1).
			- 3: Center the data around its mean.
eDim	int	3	Traditional/Cross RQA only: Embedding dimension for phase space reconstruction.
tLag	int	15	Traditional/Cross RQA only: Time lag for embedding dimensions.
rescaleNorm	int	1	Method for rescaling distances before thresholding:
			- 1: Rescale distances using the mean distance.
			- 2: Rescale distances using the maximum distance.
			- Other: Do not rescale distances (absolute thresholding).
radius	float	0.1	Recurrence radius: Threshold value for determining recurrences. Smaller values are stricter.
tw	int	2	Theiler window: Minimum time separation to exclude near-diagonal recurrences (removes artifacts).
minl	int	2	Minimum line length: The shortest line considered for calculating determinism and related metrics.
plotMode	str	'recurrence'	Specifies the type of plot to generate:
			- 'none': Do not generate plots.
			- 'rp': Basic recurrence or cross-recurrence plot only.
			- 'rp-timeseries': Plot the recurrence plot with the time series underneath or alongside.
			- 'drp': Plot recurrence for each lag in a diagonal recurrence profile.
pointSize	int	4	Size of the points in the recurrence or cross-recurrence plot.
saveFig	bool	True	Whether to save the recurrence or cross-recurrence plot:
			- True: Save plot.
			- False: Do not save plot.
showMetrics	bool	True	Whether to show RQA statistics in the console:
			- True: Show metrics in the console.
			- False: Do not show metrics in the console.
doStatsFile	bool	False	Whether to write RQA statistics to a file (RQA_Stats.csv):
			- True: Write the statistics to a file.
			- False: Do not write statistics to a file.

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Example Usage

Auto Recurrence Quantification Analysis (autoRQA)

import numpy as np
import pandas as pd
from rqa_analysis import autoRQA

# Load example data or generate sample data
data = pd.read_csv('exampleData/PostureData.csv', header=None).iloc[:, 0].values

# Set parameters
params = {
    'norm': 1,                          # Normalize to unit interval
    'eDim': 3,                          # Embedding dimension
    'tLag': 15,                         # Time lag
    'rescaleNorm': 1,                   # Rescale using mean distance
    'radius': 0.1,                      # Recurrence radius
    'tw': 2,                            # Theiler window
    'minl': 2,                          # Minimum line length
    'plotMode': 'rp-timeseries',        # Recurrence plot with time series
    'pointSize': 2,                     # Size of points in the plot
    'saveFig': False,                   # Save figure
    'showMetrics': True,                # Show metrics in the console
    'doStatsFile': False                # Write statistics to file
}

# Run Auto RQA
td, rs, mats, err_code = autoRQA(data, params)

Cross Recurrence Quantification Analysis (crossRQA)

from rqa_analysis import crossRQA

# Load synchronized data
data = pd.read_csv('exampleData/RockingChairData.csv', header=None)
data1 = data.iloc[:, 0].values  # First system
data2 = data.iloc[:, 1].values  # Second system

# Set parameters
params = {
    'norm': 1,                          # Normalize to unit interval
    'eDim': 3,                          # Embedding dimension
    'tLag': 15,                         # Time lag
    'rescaleNorm': 1,                   # Rescale using mean distance
    'radius': 0.1,                      # Recurrence radius
    'tw': 2,                            # Theiler window (not used in cross-RQA)
    'minl': 2,                          # Minimum line length
    'plotMode': 'rp-timeseries',        # Recurrence plot with time series
    'pointSize': 2,                     # Size of points in the plot
    'saveFig': False,                   # Save figure
    'showMetrics': True,                # Show metrics in the console
    'doStatsFile': False                # Write statistics to file
}

# Run Cross RQA
td, rs, mats, err_code = crossRQA(data1, data2, params)

Multivariate Recurrence Quantification Analysis (multivariateRQA) - NEW!

from rqa_analysis import multivariateRQA, multivariateCrossRQA

# Load multivariate data (e.g., 3D Lorenz chaotic system)
data = pd.read_csv('exampleData/lorenz_chaotic_xyz.csv')
multivar_data = data[['x', 'y', 'z']].values  # Use actual system dimensions

# Set parameters (no embedding needed!)
params = {
    'norm': 'zscore',                   # Z-score normalization
    'rescaleNorm': 1,                   # Rescale using mean distance
    'radius': 0.15,                     # Recurrence radius
    'tw': 1,                            # Theiler window for auto-RQA
    'minl': 2,                          # Minimum line length
    'plotMode': 'rp',                   # Recurrence plot
    'pointSize': 1,                     # Size of points in the plot
    'saveFig': False,                   # Save figure
    'showMetrics': True,                # Show metrics in the console
    'doStatsFile': False                # Write statistics to file
}

# Run Multivariate Auto-RQA
td, rs, mats, err_code = multivariateRQA(multivar_data, params)

# Or run Multivariate Cross-RQA between two systems
data1 = pd.read_csv('exampleData/lorenz_chaotic_xyz.csv')[['x', 'y', 'z']].values
data2 = pd.read_csv('exampleData/lorenz_chaotic_xyz_2.csv')[['x', 'y', 'z']].values
td, rs, mats, err_code = multivariateCrossRQA(data1, data2, params)

Key Advantages of Multivariate RQA:

• No embedding parameters (eDim, tLag) - uses actual system dimensions
• Captures true coupling between variables
• Ideal for: Coupled oscillators, multi-channel physiological signals, climate data
• Direct analysis of known multi-dimensional systems

Diagonal Recurrence Profile (DRP) - NEW!

import pandas as pd
from rqa_analysis import DRP, crossDRP

# Load example data or generate sample data
data = pd.read_csv('exampleData/PostureData.csv', header=None).iloc[:, 0].values

# Set parameters
params = {
    'norm': 1,                          # Normalize to unit interval
    'eDim': 3,                          # Embedding dimension
    'tLag': 15,                         # Time lag
    'rescaleNorm': 1,                   # Rescale using mean distance
    'radius': 0.1,                      # Recurrence radius
    'tw': 1,                            # Theiler window for auto-RQA
    'maxLag': 2000,                     # Maximum lag for DRP (auto = full time  series)
    'plotMode': 'drp',                  # Plot DRP
    'pointSize': 2,                     # Size of points in the plot
    'saveFig': False,                   # Save figure
    'showMetrics': True,                # Show metrics in the console
    'doStatsFile': False                # Write statistics to file
}

# Run Auto DRP
drp, lags = DRP(data, params)

# Or run Cross DRP between two time series
data = pd.read_csv('exampleData/RockingChairData.csv', header=None)
data1 = data.iloc[:, 0].values  # First time series
data2 = data.iloc[:, 1].values  # Second time series

drp, lags = crossDRP(data1, data2, params)

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Example Datasets

The exampleData/ folder contains diverse time series for testing and learning RQA methods:

Physiological & Experimental Data:

• PostureData.csv: Human postural sway (balance) data
• RockingChairData.csv: Interpersonal coordination between rocking chairs
• Elvis.csv: Categorical/discrete state transitions

Synthetic & Control Data:

• WhiteNoiseData.csv: Random signals for baseline comparison

Chaotic Systems (ideal for Multivariate RQA):

• lorenz_chaotic_xyz.csv: 3D Lorenz attractor (classic chaotic system)
• lorenz_chaotic_xy.csv: 2D subset for testing
• lorenz_chaotic_xyz_2.csv: Second trajectory for cross-RQA
• lorenz_hyperchaotic_xyz.csv: More complex dynamics

See exampleData/README.md for detailed descriptions and usage examples for each dataset.

Quick Start with Jupyter Notebook

Run the analysisExamples.ipynb notebook to see all RQA methods in action with real data examples, including:

• Traditional RQA on postural sway data
• Cross-RQA on interpersonal coordination
• Categorical RQA on discrete states
• Multivariate RQA on 3D chaotic systems (demonstrates the new functionality)
• Auto and Cross Diagonal Recurrence Profiles

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Related Resources

For guidance on using RQA to explore human behaviour in social and behavioural research:

• Chapter: Richardson, M. J., Dale, R., & Marsh, K. L. (2014). Complex dynamical systems in social and personality psychology. Handbook of research methods in social and personality psychology, pg. 253.

• Chapter: Macpherson, C., Richardson, M., & Kallen, R. W. (2024). Advanced quantitative approaches: Linear and non-linear time-series analyses. In Cambridge handbook of research methods and statistics for the social and behavioral sciences (Vol. 3). Cambridge University Press (CUP).

• Python tutorial: Linear and Nonlinear Time Series Analysis

References

This code is based on a matlab toolbox developed by Bruce Kay and Mike Richardson, with contributions from countless collaborators.

The implementation of multivariate RQA and Diagonal Recurrence Profiles were validated against the crqa R package developed by Coco, Mønster, Leonardi, Dale, Wallot, Dixon, Nash and Paxton.