Comprehensive HRV estimation pipeline in Python using Neurokit2: Application to sleep physiology

NeuroKit2 is a Python Toolbox for Neurophysiological Signal Processing. The presented method is an adaptation of NeuroKit2 to simplify and automate computation of the various mathematical estimates of heart rate variability (HRV) or similar time series. By default, the present approach accepts as input electrocardiogram's R-R intervals (RRIs) or peak times, i.e., timestamp of each consecutive R peak, but the RRIs or peak times can also stem from other biosensors such as photoplethysmography (PPGs) or represent more general kinds of biological or non-biological time series oscillations. The data may be derived from a single or several sources such as conventional univariate heart rate time series or intermittently weakly coupled fetal and maternal heart rate data. The method describes preprocessing and computation of an output of 124 HRV measures including measures with a dynamic, time-series-specific optimal time delay-based complexity estimation with a user-definable time window length. I also provide an additional layer of HRV estimation looking at the temporal fluctuations of the HRV estimates themselves, an approach not yet widely used in the field, yet showing promise (doi: 10.3389/fphys.2017.01112). To demonstrate the application of the methodology, I present an approach to studying the dynamic relationships between sleep state architecture and multi-dimensional HRV metrics in 31 subjects. NeuroKit2's documentation is extensive. Here, I attempted to simplify things summarizing all you need to produce the most extensive HRV estimation output available to date as open source and all in one place. The presented Jupyter notebooks allow the user to run HRV analyses quickly and at scale on univariate or multivariate time-series data. I gratefully acknowledge the excellent support from the NeuroKit team.•Univariate or multivariate time series input; ingestion, preprocessing, and computation of 124 HRV metrics.•Estimation of intra- and inter-individual higher order temporal fluctuations of HRV metrics.•Application to a sleep dataset recorded using Apple Watch and expert sleep labeling.