PhysioScripts: An extensible, open source platform for the processing of physiological data

A commonality across research involving physiological measures is the need to process large amounts of data. Such data processing typically involves the use of software tools to achieve several methodological steps, including identifying and correcting artifacts and defining epochs of time for the reduction and analysis of one or more physiological measures. This article describes a new tool to aid in the processing of physiological data: PhysioScripts. Key elements of PhysioScripts include a graphical interface to view and edit the results of processing steps, as well as a flexible framework to automate the creation of uniform or variable length epochs. The software comprises freely available scripts implemented in the R computing environment. Consequently, PhysioScripts can be readily modified to process other data types through the addition of new subroutines that can be plugged into the existing data processing framework. For illustrative purposes, we describe the steps involved in two data processing examples: (1) heart rate variability from the electrocardiogram and (2) respiratory rate derived from a chest strain gauge. The software, accompanying documentation, and an example data set are available online at israelchristie.com/software.