mhrv.hrv

hrv_time()

mhrv.hrv.hrv_time(nni, varargin)

Calculates time-domain HRV mertics from NN intervals.

Parameters
  • nni – Vector of NN-interval dirations (in seconds)

  • varargin

    Pass in name-value pairs to configure advanced options:

    • pnn_thresh_ms: Optional. Threshold NN interval time difference in milliseconds (for the pNNx HRV measure).

    • plot: true/false whether to generate a plot. Defaults to true if no output arguments were specified.

Returns

Table containing the following HRV metrics:

  • AVNN: Average NN interval duration.

  • SDNN: Standard deviation of NN interval durations.

  • RMSSD: Square root of mean summed squares of NN interval differences.

  • pNNx: The percentage of NN intervals which differ by at least x (ms) (default 50) from their preceding interval. The value of x in milliseconds can be set with the optional parameter ‘pnn_thresh_ms’.

  • SEM: Standard error of the mean NN interval length.

hrv_freq()

mhrv.hrv.hrv_freq(nni, varargin)

NN interval spectrum and frequency-domain HRV metrics This function estimates the PSD (power spectral density) of a given nn-interval sequence, and calculates the power in various frequency bands.

Parameters
  • nni – RR/NN intervals, in seconds.

  • varargin

    Pass in name-value pairs to configure advanced options:

    • methods: A cell array of strings containing names of methods to use to estimate the spectrum. Supported methods are:

      • lomb: Lomb-scargle periodogram.

      • ar: Yule-Walker autoregressive model. Data will be resampled. No windowing will be performed for this method.

      • welch: Welch’s method (overlapping windows).

      • fft: Simple fft-based periodogram, no overlap (also known as Bartlett’s method).

      In all cases, a window will be used on the samples according to the win_func parameter. Data will be resampled for all methods except lomb. Default value is {'lomb', 'ar', 'welch'}.

    • time_intervals: specify the time interval vector tnn. If it is not specified then it will be computed from the nni time series.

    • power_methods: The method(s) to use for calculating the power in each band. A cell array where each element can be any one of the methods given in ‘methods’. This also determines the spectrum that will be returned from this function (pxx). Default: First value in methods.

    • norm_method: A string, either total or lf_hf. If total, then the power in each band will be normalized by the total power in the entire frequency spectrum. If lf_hf, then only for the LF and HF bands, the normalization will be performed by the (LF+HF) power. This is the standard method used in many papers to normalize these bands. In any case, VLF and user-defined custom bands are not affected by this parameter.

    • band_factor: A factor that will be applied to the frequency bands. Useful for shifting them linearly to adapt to non-human data. Default: 1.0 (no shift).

    • vlf_band: 2-element vector of frequencies in Hz defining the VLF band. Default: [0.003, 0.04].

    • lf_band: 2-element vector of frequencies in Hz defining the LF band. Default: [0.04, 0.15].

    • hf_band: 2-element vector of frequencies in Hz defining the HF band. Default: [0.15, 0.4].

    • extra_bands: A cell array of frequency pairs, for example {[f_start,f_end], ...}. Each pair defines a custom band for which the power and normalized power will be calculated.

    • window_minutes: Split intervals into windows of this length, calcualte the spectrum in each window, and average them. A window funciton will be also be applied to each window after breaking the intervals into windows. Set to [] if you want to disable windowing. Default: 5 minutes.

    • detrend_order: Order of polynomial to fit to the data for detrending. Default: 1 (i.e. linear detrending).

    • ar_order: Order of the autoregressive model to use if ar method is specific. Default: 24.

    • welch_overlap: Percentage of overlap between windows when using Welch’s method. Default: 50 percent.

    • win_func: The window function to apply to each segment. Should be a function that accepts one parameter (length in samples) and returns a window of that length. Default: @hamming.

    • plot: true/false whether to generate plots. Defaults to true if no output arguments were specified.

Returns

  • hrv_fd: Table containing the following HRV metrics:

    • TOTAL_POWER: Total power in all three bands combined.

    • VLF_POWER: Power in the VLF band.

    • LF_POWER: Power in the LF band.

    • HF_POWER: Power in the HF band.

    • VLF_NORM: 100 * Ratio between VLF power and total power.

    • LF_NORM: 100 * Ratio between LF power and total power or the sum of LF and HF power (see ‘norm_method’). - HF_NORM: 100 * Ratio between HF power and total power or the sum of LF and HF power (see norm_method).

    • LF_TO_HF: Ratio between LF and HF power.

    • LF_PEAK: Frequency of highest peak in the LF band.

    • HF_PEAK: Frequency of highest peak in the HF band.

    • BETA: Slope of log-log frequency plot in the VLF band.

    Note that each of the above metrics will be calculated for each value given in power_methods, and their names will be suffixed with the method name (e.g. LF_PEAK_LOMB).

  • pxx: Power spectrum. It’s type is determined by the first value in power_methods.

  • f_axis: Frequencies, in Hz, at which pxx was calculated.

hrv_nonlinear()

mhrv.hrv.hrv_nonlinear(nni, varargin)

Calcualtes non-linear HRV metrics based on Poincaré plots, detrended fluctuation analysis (DFA) 2 and Multiscale Entropy (MSE) 3.

Parameters
  • nni – RR/NN intervals, in seconds.

  • varargin

    Pass in name-value pairs to configure advanced options:

    • mse_max_scale: Maximal scale value that the MSE will be calculated up to.

    • mse_metrics: Whether to output MSE at each scale as a separate metric.

    • sampen_r: r value used to calculate Sample Entropy

    • sampen_m: m value used to calculate Sample Entropy

    • plot: true/false whether to generate plots. Defaults to true if no output arguments were specified.

Returns

  • hrv_nl: Table containing the following HRV metrics:

    • SD1: Poincare plot SD1 descriptor (std. dev. of intervals along the line perpendicular to the line of identity).

    • SD2: Poincare plot SD2 descriptor (std. dev. of intervals along the line of identity).

    • alpha1: Log-log slope of DFA in the low-scale region.

    • alpha2: Log-log slope of DFA in the high-scale region.

    • SampEn: The sample entropy.

2

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.

3

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.

hrv_fragmentation()

mhrv.hrv.hrv_fragmentation(nni, varargin)

Computes HRV fragmentation indices 1 of a NN interval time series.

Parameters

nni – Vector of NN-interval dirations (in seconds)

Returns

Table containing the following fragmentation metrics:

  • PIP: Percentage of inflection points.

  • IALS: Inverse average length of segments.

  • PSS: Percentage of NN intervals that are in short segments.

  • PAS: Percentage of NN intervals that are in alternation segments of at least 4 intervals.

1

Costa, M. D., Davis, R. B., & Goldberger, A. L. (2017). Heart Rate Fragmentation: A New Approach to the Analysis of Cardiac Interbeat Interval Dynamics. Frontiers in Physiology, 8(May), 1–13.