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Permutation entropy (fast algorithm)

version 1.5.3 (815 KB) by Valentina Unakafova
Efficiently computing values of permutation entropy from 1D time series in sliding windows

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Updated 15 Oct 2018

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function outdata = PE( indata, delay, order, windowSize )
computes efficiently [1] values of permutation entropy [2] for orders=1...8 of ordinal patterns from 1D time series in sliding windows. See more ordinal-patterns based measures at www.mathworks.com/matlabcentral/fileexchange/63782-ordinal-patterns-based-analysis--beta-version-

NOTES
1 Order of ordinal patterns is defined as in [1,3,7,8], i.e. order = n-1 for n defined as in [2]
2 The values of permutation entropy are normalised by log((order+1)!) so that they are from [0,1] as proposed in the original paper [2].

INPUT
- indata - 1D time series (1 x N points)
- delay - delay between points in ordinal patterns (delay = 1 means successive points)
- order - order of the ordinal patterns (order + 1 is the number of points in ordinal patterns)
- windowSize - size of sliding window ( = number of ordinal patterns within sliding window)

OUTPUT
- outdata - (1 x (N - windowSize - order*delay) values of permutation entropy within [0,1] since each sliding window contains windowSize ordinal patterns but uses in fact (windowSize + order*delay + 1) points).

INTERPRETATION
The larger the values of permutation entropy (in the range from 0 to 1) are, the higher diversity of ordinal patterns is and the more complex input data are.

CITING THE CODE
[a] Unakafova, V.A., Keller, K., 2013. Efficiently measuring complexity on the basis of real-world data. Entropy, 15(10), 4392-4415.
[b] Unakafova, Valentina (2015). Fast permutation entropy (www.mathworks.com/matlabcentral/fileexchange/44161-permutation-entropy--fast-algorithm-), MATLAB Central File Exchange. Retrieved Month Day, Year.

EXAMPLE OF USE (with a plot):
indata = rand( 1, 7777 ); % generate random data points
for i = 4000:7000 % generate change of data complexity
indata( i ) = 4*indata( i - 1 )*( 1 - indata( i - 1 ) );
end
delay = 1; % delay 1 between points in ordinal patterns (successive points)
order = 3; % order 3 of ordinal patterns (4-points ordinal patterns)
windowSize = 512; % 512 ordinal patterns in one sliding window
outdata = PE( indata, delay, order, windowSize );
figure;
ax1 = subplot( 2, 1, 1 ); plot( indata, 'k', 'LineWidth', 0.2 );
grid on; title( 'Original time series' );
ax2 = subplot( 2, 1, 2 );
plot( length(indata) - length(outdata)+1:length(indata), outdata, 'k', 'LineWidth', 0.2 );
grid on; title( 'Values of permutation entropy' );
linkaxes( [ ax1, ax2 ], 'x' );

CHOICE OF ORDER OF ORDINAL PATTERNS
The larger order of ordinal patterns is, the better permutation entropy estimates complexity of the underlying dynamical system [3]. But for time series of finite length too large order of ordinal patterns leads to an underestimation of the complexity because not all ordinal patterns representing the system can occur [3]. Therefore, for practical applications, orders = 3...7 are often used [2,4,5,8].
In [6] the following rule for choice of order is recommended:
5*(order + 1)! < windowSize.

CHOICE OF SLIDING WINDOW LENGTH
Window size should be chosen in such way that time series is stationary within the window (for example, for EEG analysis 2 seconds sliding windows are often used) so that distribution of ordinal patterns would not change within the window [2,8], [3,Section 2.2], [7,Section 5.1.2].

CHOICE OF DELAY BETWEEN POINTS IN ORDINAL PATTERNS
I would recommend choosing different delays and comparing results (see, for example, [3, Section 2.2-2.4] and [7, Chapter 5] for more details) though delay = 1 is often used for practical applications.
Choice of delay depends on particular data analysis you perform [3,4], on type of pre-processing and on sampling rate of the data. For example, if you are interested in low-frequency part of signals it makes sense to use larger delays.

REFERENCES
[1] Unakafova, V.A., Keller, K., 2013. Efficiently measuring complexity on the basis of real-world Data. Entropy, 15(10), 4392-4415.
[2] Bandt, C. and Pompe, B., 2002. Permutation entropy: a natural complexity measure for time series. Physical review letters, 88(17), p.174102.
[3] Keller, K., Unakafov, A.M. and Unakafova, V.A., 2014. Ordinal patterns, entropy, and EEG. Entropy, 16(12), pp.6212-6239.
[4] Riedl, M., Muller, A. and Wessel, N., 2013. Practical considerations of permutation entropy. The European Physical Journal Special Topics, 222(2), pp.249-262.
[5] Zanin, M., Zunino, L., Rosso, O.A. and Papo, D., 2012. Permutation entropy and its main biomedical and econophysics applications: a review. Entropy, 14(8), pp.1553-1577.
[6] Amigo, J.M., Zambrano, S. and Sanjuan, M.A., 2008. Combinatorial detection of determinism in noisy time series. EPL (Europhysics Letters), 83(6), p.60005.
[7] Unakafova, V.A., 2015. Investigating measures of complexity for dynamical systems and for time series (Doctoral dissertation, University of Luebeck).
[8] Keller, K., and M. Sinn. Ordinal analysis of time series. Physica A: Statistical Mechanics and its Applications 356.1 (2005): 114—120

Cite As

Valentina Unakafova (2019). Permutation entropy (fast algorithm) (https://www.mathworks.com/matlabcentral/fileexchange/44161-permutation-entropy-fast-algorithm), MATLAB Central File Exchange. Retrieved .

Comments and Ratings (4)

Fulin Cai

citysky

MM xu

ervin

Updates

1.5.3

Cover pictures has been updated

1.5.2.1

The files have also been uploaded at GitHub: https://github.com/ValentinaUn/Fast-permutation-entropy

1.5.2.0

Description has been renewed (section INTERPRETATION has been added)

1.5.1.0

Description (NOTES section) has been updated

1.5.0.0

1 The script is updated for compatibility with MATLAB 2018.
2 The values of permutation entropy are normalised as in the original paper by Bandt and Pompe (divided by log((order+1)!)) not by the order of ordinal patterns as in the previous version.

1.4.3.3

Two variables are renamed in the m-file for consistency.

1.4.3.2

Description has been renewed

1.4.3.1

Description is renewed (notes on parameters choice are added)

1.4.3.0

description is renewed

1.4.2.0

Example of use is corrected

1.4.1.0

Example of use is corrected

1.4.0.0

Example of use is added

1.3.0.0

1 The values of permutation entropy are divided by order of ordinal patterns
2 Minor code style corrections

1.2.0.0

-

1.2.0.0

-

1.1.0.0

A small mistake in the code is corrected:
(line 49) iTau = 1;
is replaced by
(line 48) iTau = mod(WS, Tau)+1;

This mistake introduced a small (~1%) error only in the first WS ePE values if computing for tau>1.

MATLAB Release Compatibility
Created with R2012b
Compatible with any release
Platform Compatibility
Windows macOS Linux