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Research accelerometers: ActiGraph and Axivity

Source: vignettes/research-accelerometers.Rmd
research-accelerometers.Rmd
library(PhysioDevices)
#> Loading required package: PhysioCore

readGT3X() and readCWA() read the two field-standard raw research accelerometers – ActiGraph (.gt3x, common in US cohorts) and Axivity AX3/AX6 (.cwa, used by UK Biobank and other large studies) – into the same tri-axial-acceleration PhysioExperiment that PhysioWearable::readAccelCSV() produces, so they flow straight into the free-living pipeline.

The binary decode is delegated to the validated read.gt3x and GGIRread packages (install them first); the readers only adapt the result.

pe <- readGT3X("subject.gt3x")          # or readCWA("subject.cwa")
pe                                       # a PhysioExperiment: acceleration (x/y/z, g)
samplingRate(pe)

Free-living metrics

The acceleration assay feeds ENMO, non-wear/calibration, intensity and the free-living summary exactly as for readAccelCSV() output:

acc  <- SummarizedExperiment::assay(pe, "acceleration")
enmo <- PhysioWearable::computeENMO(acc, sampling_rate = samplingRate(pe))
PhysioWearable::summarizeFreeLiving(enmo)          # wear time, MVPA, intensity gradient, ...

Notes

  • read.gt3x / GGIRread are Suggests – each reader errors with an install hint if its package is missing.
  • readCWA() reads the whole file by default; pass start/end (block range) to read a long recording in pieces.
  • These devices record raw acceleration only (no HR/SpO2); pair them with a smartwatch reader for those signals.