mhrv is a matlab toolbox for calculating Heart-Rate Variability (HRV) metrics
from both ECG signals and RR-interval time series. The toolbox works with ECG
data in the PhysioNet  WFDB data format.
WFDB wrappers and helpers. A small subset of the PhysioNet WFDB tools are wrapped with matlab functions, to allow using them directly from matlab.
gqrs- A QRS detection algorithm.
rdsamp- For reading PhysioNet signal data into matlab.
rdann- For reading PhysioNet annotation data into matlab.
wrann- For writing PhysioNet annotation data from matlab datatypes.
wfdb_header- Read record metadata from a WFDB header file (
ECG signal processing. Peak detection and RR interval extraction from ECG data in PhysioNet format.
rqrs- Detection of R-peaks in ECG signals (based on PhysioNet's
gqrs). Configurable for use with both human and animal ECGs.
wjqrs- An ECG peak-detector based on a modified Pan & Tompkins algorithm and a windowed version.
bpfilt- Bandpass filtering for removing noise artifacts from ECG signals.
ecgrr- Construction of RR intervals from ECG data in PhysioNet format.
qrs_compare- Comparison of QRS detections to reference annotations and calculation of quality measures like Sensitivity, PPV.
RR-intervals signal processing. Ectopic beat rejection, frequency filtering, nonlinear dynamic and fractal analysis.
filtrr- Filtering of RR interval time series to detect ectopic (out of place) beats.
dfa- Detrended Fluctuation Analysis, a method of estimating the fractal scaling exponent of a signal .
mse- Multiscale Sample Entropy, a measure of the complexity of the signal computed on multiple time scales .
sample_entropy- Sample Entropy, a measure of the irregularity of a signal.
HRV Metrics: Calculating quantitative measures that indicate the activity of the heart based on RR intervals using all standard HRV metrics defined in the literature (see e.g. ).
hrv_time- Time Domain: AVNN, SDNN, RMSSD, pNNx.
hrv_freq- Frequency Domain:
- Total and normalized power in (configurable) VLF, LF, HF and custom user-defined bands.
- Spectral power estimation using Lomb, Auto Regressive, Welch and FFT methods.
- Additional frequency-domain features: LF/HF ratio, LF and HF peak frequencies, power-law scaling exponent (beta).
hrv_nonlinear- Nonlinear methods:
- Short- and long-term scaling exponents (alpha1, alpha2) based on DFA.
- Sample Entropy and Multiscale sample entropy (MSE).
- Poincaré plot metrics (SD1, SD2).
hrv_fragmentation- Time-domain RR interval fragmentation analysis .
Configuration: The toolbox is fully configurable with many user-adjustable parameters.
- The configuration files are in human-readable YAML format which is easy to edit and extend.
- The user can create custom configurations files based on the
defatuls.ymlfile (only overriding what's required).
- Custom configuration files can be loaded with a single call which updates the defaults for the entire toolbox. This allows simple, reproducible analysis of different datasets that require different analysis configurations.
- The settings for any of the functions can either be configured globally
ymlfiles or on a per-call basis with matlab-style key-value argument pairs.
Plotting: All toolbox functions support plotting their output for data visualization. The plotting code is separated from the algorithmic code in order to simplify embedding this toolbox in other matlab applications.
Top-level analysis functions: These functions work with PhysioNet records and allow streamlined HRV analysis by composing the functions of this toolbox.
mhrv- Analyzes a single PhysioNet record (ECG data or annotations), optionally split into multiple analysis windows. Extracts all supported HRV features and optionally generates plots.
mhrv_batch- Analyzes many PhysioNet records (ECG data or annotations) which can be further separated into user-defined groups (e.g. Control, Test). Automatically computes HRV metrics per group and generates a comparative summary of the HRV features in each group.
- Matlab with Signal Processing toolbox. Should work on Matlab R2014b or newer.
- The PhysioNet WFDB tools. The toolbox can install this for you.
Clone the repo or download the source code.
From MATLAB, run the
mhrv_initfunction. This function will:
- Check for the presence of the WFDB tools in your system
PATH. If WFDB tools are not detected, it will attempt to automatically download them for you into the folder
bin/wfdbunder the repository root.
- Set up your MATLAB path to include the code from this toolbox.
- Check for the presence of the WFDB tools in your system
Manual WFDB Installation (Optional)
The above steps should be enough to get most users started. If however you
mhrv_init to download the WFDB tools for you, or the automatic
installation fails for some reason, you can install them yourself.
- On OSX, you can use homebrew to install it easily with
brew install wfdb.
- On Windows and Linux, you should either download the WFDB binaries for your OS or compile them from source using the instructions on their website.
Once you have the binaries, place them in some folder on your
somewere under the repo's root folder (
bin/wfdb would be a good choice as it's
.gitignored) and they will be found and used automatically. Or, if you would
like to manually specify a path outside the repo which contains the WFDB
/usr/local/bin for a homebrew install), you can edit
and set the
mhrv.paths.wfdb_path variable to the desired path.
For linux users it's recommended to install from source as the binaries provided on the PhysioNet website are very outdated.
Documentation is available on readthedocs.
Exaple of calculating HRV measures for a PhysioNet record downloaded from
PhysioNet (in this case from
% Download the mitdb/111 record from PhysioNet to local folder named 'db' >> download_wfdb_records('mitdb', '111', 'db'); % Run HRV analysis >> mhrv('db/mitdb/111', 'window_minutes', 15, 'plot', true);
Will give you:
[0.000] >> mhrv: Processing ECG signal from record db/mitdb/111 (ch. 1)... [0.000] >> mhrv: Signal duration: 00:30:05.000 [HH:mm:ss.ms] [0.010] >> mhrv: Analyzing window 1 of 2... [0.010] >> mhrv: [1/2] Detecting QRS end RR intervals... [0.810] >> mhrv: [1/2] Filtering RR intervals... [0.840] >> mhrv: [1/2] 1039 NN intervals, 6 RR intervals were filtered out [0.840] >> mhrv: [1/2] Calculating time-domain metrics... [0.920] >> mhrv: [1/2] Calculating frequency-domain metrics... [1.180] >> mhrv: [1/2] Calculating nonlinear metrics... [1.430] >> mhrv: [1/2] Calculating fragmentation metrics... [1.490] >> mhrv: Analyzing window 2 of 2... [1.490] >> mhrv: [2/2] Detecting QRS end RR intervals... [2.080] >> mhrv: [2/2] Filtering RR intervals... [2.100] >> mhrv: [2/2] 1057 NN intervals, 8 RR intervals were filtered out [2.100] >> mhrv: [2/2] Calculating time-domain metrics... [2.140] >> mhrv: [2/2] Calculating frequency-domain metrics... [2.240] >> mhrv: [2/2] Calculating nonlinear metrics... [2.450] >> mhrv: [2/2] Calculating fragmentation metrics... [2.490] >> mhrv: Building statistics table... [2.520] >> mhrv: Displaying Results... RR NN AVNN SDNN RMSSD pNN50 SEM TOTAL_POWER_LOMB VLF_POWER_LOMB LF_POWER_LOMB HF_POWER_LOMB LF_NORM_LOMB HF_NORM_LOMB LF_TO_HF_LOMB LF_PEAK_LOMB HF_PEAK_LOMB SD1 SD2 alpha1 alpha2 beta SampEn PIP IALS PSS PAS ____ ____ ______ ______ ______ _______ _______ ________________ ______________ _____________ _____________ ____________ ____________ _____________ ____________ ____________ _______ ______ ________ ________ _______ _______ _______ _________ ______ ______ 1 1045 1039 858.96 30.961 33.622 14.162 0.96054 333.22 67.098 23.574 242.55 8.8583 91.142 0.097193 0.046667 0.16667 23.786 36.745 0.65937 0.72845 -1.2471 1.835 53.321 0.53468 61.598 12.512 2 1065 1057 841.86 40.182 32.306 12.784 1.2359 388.66 132.7 32.031 223.93 12.514 87.486 0.14304 0.043333 0.16667 22.855 51.996 0.70064 0.92309 -1.6706 1.6483 52.318 0.52462 57.332 15.137 Mean 1055 1048 850.41 35.572 32.964 13.473 1.0982 360.94 99.899 27.802 233.24 10.686 89.314 0.12012 0.045 0.16667 23.32 44.371 0.68 0.82577 -1.4588 1.7417 52.819 0.52965 59.465 13.825 SE 10 9 8.5503 4.6103 0.6578 0.68888 0.1377 27.723 32.801 4.2286 9.3065 1.8278 1.8278 0.022923 0.0016667 0 0.46545 7.6255 0.020637 0.097316 0.21176 0.09336 0.50131 0.0050304 2.1328 1.3126 Median 1055 1048 850.41 35.572 32.964 13.473 1.0982 360.94 99.899 27.802 233.24 10.686 89.314 0.12012 0.045 0.16667 23.32 44.371 0.68 0.82577 -1.4588 1.7417 52.819 0.52965 59.465 13.825 [2.580] >> mhrv: Generating plots... [4.930] >> mhrv: Finished processing record db/mitdb/111.
window_minutes parameter allow splitting the signal into windows and
calculating all metrics per window. You can pass in an empty array
Example plots (generated by the example above):
- ECG R-peak detection
- RR interval time series filtering
- Time-domain HRV Metrics
- Spectrum of interval time series
- Nonlinear HRV Metrics
- Poincaré plot and ellipse fitting
This toolbox, initially called
rhrv, was created as part of my MSc research
thesis. It was then renamed and updated to be used as the basis of the
PhysioZoo platform for HRV analysis of human and
To use it in you own research, please cite:
Rosenberg, A. A. (2018) ‘Non-invasive in-vivo analysis of intrinsic clock-like pacemaker mechanisms: Decoupling neural input using heart rate variability measurements.’ MSc Thesis. Technion, Israel Institute of Technology.
Behar J. A., Rosenberg A. A. et. al. (2018) ‘PhysioZoo: a novel open access platform for heart rate variability analysis of mammalian electrocardiographic data.’ Frontiers in Physiology.
Several other projects exist with various levels of overlapping functionality and purpose.
- The PhysioNet WFDB tools.
- The WFDB toolbox for matlab.
- The R-HRV toolbox for the R language.
- The Kubios software package.
- The PhysioZoo platform for mammalian ECG and HRV analysis.
Some of the code in
lib/ was created by others, used here as dependencies.
Original author attribution exists in the source files.
Feel free to send pull requests or open issues via GitHub.
- Goldberger, A. L. et al. (2000) ‘PhysioBank, PhysioToolkit, and PhysioNet’, Circulation, 101(23), pp. E215-20.
- Task Force of the European Society of Cardiology and the North American Society of Pacing and Electrophysiology. (1996) ‘Heart rate variability. Standards of measurement, physiological interpretation, and clinical use.’, European Heart Journal, 17(3), pp. 354–81.
- Peng, C.-K., Hausdorff, J. M. and Goldberger, A. L. (2000) ‘Fractal mechanisms in neuronal control: human heartbeat and gait dynamics in health and disease, Self-organized biological dynamics and nonlinear control.’ Cambridge: Cambridge University Press.
- Costa, M. D., Goldberger, A. L. and Peng, C.-K. (2005) ‘Multiscale entropy analysis of biological signals’, Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 71(2), pp. 1–18.
- Costa, M. D., Davis, R. B. and Goldberger, A. L. (2017) ‘Heart Rate Fragmentation : A New Approach to the Analysis of Cardiac Interbeat Interval Dynamics’, Frontiers in Physiology, 8(May), pp. 1–13.