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Tracking the autonomic control and respiratory sinus arrhythmia (RSA) from electrocardiogram and respiratory measurements is an important problem in cardiovascular control. We propose a point process adaptive filter algorithm based on an inverse Gaussian model to track heart beat intervals that incorporates respiratory measurements as a covariate and provides an analytic form for computing a dynamic estimate of RSA gain. We use Kolmogorov-Smirnov tests and autocorrelation function analyses to assess model goodness-of-fit. We illustrate the properties of the new dynamic estimate of RSA in the analysis of simulated heart beat data and actual heart beat data recorded from subjects in a four-state postural study of heart beat dynamics: control, sympathetic blockade, parasympathetic blockade, and combined sympathetic and parasympathetic blockade. In addition to giving an accurate description of the heart beat data, our adaptive filter algorithm confirms established findings pointing at a vagally mediated RSA and provides a new dynamic RSA estimate that can be used to track cardiovascular control between and within a broad range of postural, pharmacological, and age conditions. Our paradigm suggests a possible framework for designing a device for ambulatory monitoring and assessment of autonomic control in both laboratory research and clinical practice.