Processing of Accelerometry Data with GGIR in Motor Activity Research Consortium for Health

The Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of clinical and community studies that employ common digital mobile protocols and collect common clinical and biological measures across participating studies. At a high level, a key scientific goal which spans mMARCH studies is to develop a better understanding of the interrelationships between physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. mMARCH studies employ wrist-worn accelerometry to obtain objective measures of PA/SL/ CR. However, there is currently no consensus on a standard data processing pipeline for raw accelerometry data and few opensource tools which facilitate their development. The R package GGIR is the most prominent open-source software package for processing raw accelerometry data, offering great functionality and substantial user flexibility. However, even with GGIR, processing done in a harmonized and reproducible fashion across multiple analytical centers requires a nontrivial amount of expertise combined with a careful implementation. In addition, there are many statistical methods useful for analyzing PA/SL/CR patterns using accelerometry data which are implemented in non-GGIR R packages, including methods from multivariate statistics, functional data analysis, distributional data analysis, and time series analyses. To address the issues of multisite harmonization and additional feature creation, mMARCH developed a streamlined harmonized and reproducible pipeline for loading and cleaning raw accelerometry data via GGIR, merging GGIR, and non-GGIR features of PA/SL/CR together, implementing several additional data and feature quality checks, and performing multiple analyses including Joint and Individual Variation Explained, an unsupervised machine learning dimension reduction technique that identifies latent factors capturing joint across and individual to each of three domains of PA/SL/CR. The pipeline is easily modified to calculate additional features of interest, and allows for studies not affiliated with mMARCH to apply a pipeline which facilitates direct comparisons of scientific results in published work by mMARCH studies. This manuscript describes the pipeline and illustrates the use of combined GGIR and non-GGIR features by applying Joint and Individual Variation Explained to the accelerometry component of CoLaus|PsyCoLaus, one of mMARCH sites. The pipeline is publicly available via open-source R package mMARCH.AC.