defaults.yml

# Default parameter values of the mhrv toolbox
---

# Peak detection
rqrs:
    use_gqpost:
        value: false
        description: Wheter to use gqpost for peak detection post-processing
        name: Use gqpost
        units: boolean
    gqconf:
        value: gqrs.default.conf
        description: Path to gqrs config file
        name: gqconf path
    window_size_sec:
        value: 0.056
        description: Size of rqrs forward-search window
        name: rqrs Window Size
        units: Seconds

# RR Interval filtering
filtrr:
    range:
        enable:
            value: true
            description: Whether to enable range-based filtering
            name: Enable range filter
            units: boolean
        rr_min:
            value: 0.32
            description: Minimal allowed RR interval duration
            name: RR min
            units: Seconds
        rr_max:
            value: 1.5
            description: Maximal allowed RR interval duration
            name: RR max
            units: Seconds
    moving_average:
        enable:
            value: true
            description: Whether to enable moving average-based filtering
            name: Enable moving average filter
            units: boolean
        win_length:
            value: 10
            description: Length in samples of the moving average filter
            name: Moving average filter length
            units: Samples
        win_threshold:
            value: 20
            description: Threshold percantage above/below the moving average filter value.
            name: Moving average filter threshold
            units: '%'
    quotient:
        enable:
            value: true
            description: Whether to enable quotient filter
            name: Enable quotient filter
            units: boolean
        rr_max_change:
            value: 25
            description: Maximal allowed change between adjacent RR intervals
            name: RR max change
            units: '%'

# Time-domain HRV parameters
hrv_time:
    pnn_thresh_ms:
        value: 50
        description: Threshold value for PNNx
        name: PNN Threshold
        units: Milliseconds

# Frequency-domain HRV parameters
hrv_freq:
    methods:
        value: [lomb, ar, welch]  # possible methods: 
        description: Methods of spectral calculation (can be lomb/ar/welch/fft)
        name: Spectrum types
    power_methods:
        value: [] # Empty means first method in 'methods'
        description: Spectrums to calculate power from
        name: Spectrums for power calculation
    norm_method:
        value: total # total, lf_hf
        description: How to normalize the LF and HF bands
        name: LF and HF band normalization method
        units: ''
    beta_band:
        value: []
        description: Frequency band range for beta calculation (empty = use VLF band)
        name: Beta Band
        units: Hz
    vlf_band:
        value: [0.003, 0.04]
        description: VLF frequency band range
        name: VLF Band
        units: Hz
    lf_band:
        value: [0.04,  0.15]
        description: LF frequency band range
        name: LF Band
        units: Hz
    hf_band:
        value: [0.15,  0.4]
        description: HF frequency band range
        name: HF Band
        units: Hz
    extra_bands:
        value: []
        description: Additional frequency bands for power calculation (each element should be a two-element array)
        name: Extra bands
        units: Hz
    window_minutes:
        value: 5
        description: Duration of winodow for spectral averaging
        name: Spectral window duration
        units: Minutes
    welch_overlap:
        value: 50
        description: Percent overlap between windows when using welch method
        name: Welch overlap
        units: '%'
    ar_order:
        value: 24
        description: Order of AR model to fit
        name: AR order
        units: n.u.
    osf:
        value: 4
        description: Factor of oversampling in frequency domain resolution
        name: Frequency oversampling factor
        units: n.u.
    resample_factor:
        value: 2.25
        description: Factor of f_max (hf_band(2)) to obtain the uniform sampling frequecncy. Must be >= 2.
        name: Frequency resampling factor
        units: n.u.
    win_func:
        value: hamming
        description: Name of window to apply to segments. Should be one of the matlab window functions.
        name: Window function.
        units: n.u.

# DFA Parameters
dfa:
    n_min:
        value: 4
        description: Minimal DFA box size
        units: n.u.
    n_max:
        value: 64
        description: Maximal DFA box size
        units: n.u.
    n_incr:
        value: 2
        description: DFA box size increment
        units: n.u.
    alpha1_range:
        value: [4, 15]
        description: Box size range for alpha1 slope calculation
        name: Alpha1 range
        units: n.u.
    alpha2_range:
        value: [16, 64]
        description: Box size range for alpha2 slope calculation
        name: Alpha2 range
        units: n.u.

# MSE Parameters
mse:
    mse_max_scale:
        value: 15
        description: Maximal scale value for MSE calculation
        name: MSE max scale
        units: n.u.
    sampen_r:
        value: 0.2
        description: Sample entropy template match threshold
        name: SampEn r
        units: n.u.
    sampen_m:
        value: 2
        description: Sample entropy template length
        name: SampEn m
        units: n.u.
    normalize_std:
        value: true
        description: Whether to normalize the signal to std=1 before calculating MSE.
        name: Normalize Standard Deviation
        units: boolean
    mse_metrics:
        value: false
        description: Whether to output each MSE value as a metric
        name: Output MSE metrics
        units: boolean

# General toolbox options
mhrv:
    paths:
        wfdb_path: ''