Analysis package for actigraphy data
Project description
pyActigraphy
Open-source python package for actigraphy data visualization and analysis.
This package is meant to provide a comprehensive set of tools to:
read native actigraphy data files with various formats:
Actigraph: wGT3X-BT
CamNtech: Actiwatch 4 and MotionWatch 8
Condor Instrument: ActTrust 2
Daqtix: Daqtometer
Respironics: Actiwatch 2 and Actiwatch Spectrum (plus)
Tempatilumi (CE Brasil)
clean the raw data and mask spurious periods of inactivity
produce activity profile plots
visualize sleep agendas and compute summary statistics
calculate typical wake/sleep cycle-related variables:
Non-parametric rest-activity variables: IS(m), IV(m), RA
Activity or Rest fragmentation: kRA, kAR
Sleep regularity index (SRI)
automatically detect rest periods using various algorithms (Cole-Kripke, Sadeh, …, Crespo, Roenneberg)
perform complex analyses:
Cosinor analysis
Detrended Fluctuation Analysis (DFA)
Functional Linear Modelling (FLM)
Locomotor Inactivity During Sleep (LIDS)
Singular Spectrum Analysis (SSA)
and much more…
Code and documentation
The pyActigraphy package is open-source and its source code is accessible online.
An online documentation of the package is also available here. It contains notebooks illustrating various functionalities of the package.
Installation
In a (bash) shell, simply type:
For users:
pip3 install pyActigraphy
To update the package:
pip3 install -U pyActigraphy
For developers:
git clone git@github.com:ghammad/pyActigraphy.git
cd pyActigraphy/
git checkout develop
pip3 install -e .
Quick start
The following example illustrates how to calculate the interdaily stability with the pyActigraphy package:
>>> import pyActigraphy
>>> rawAWD = pyActigraphy.io.read_raw_awd('/path/to/your/favourite/file.AWD')
>>> rawAWD.IS()
0.6900175913031027
>>> rawAWD.IS(freq='30min', binarize=True, threshold=4)
0.6245582891144925
>>> rawAWD.IS(freq='1H', binarize=False)
0.5257020914453097
Contributing
There are plenty of ways to contribute to this package, including (but not limiting to):
report bugs (and, ideally, how to reproduce the bug)
suggest improvements
improve the documentation
License
This project is licensed under the GNU GPL-3.0 License - see the LICENSE file for details
Acknowledgments
Aubin Ardois @aardoi developed the first version of the MTN class during his internship at the CRC, in May-August 2018.
The CRC colleagues for their support, ideas, etc.
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