Sedentary-Time Analysis

This repository provides the paper code and rendered outputs for estimating waking sedentary time in NHANES 2011-2014 wrist accelerometer data.

It offers:

• one reproducible analysis report;
• final manuscript tables and figures;
• final CSV outputs used by the report;
• the small local files needed for sleep calibration and the workflow figure.

Paper

Sedentary Behavior in the United States Measured by Accelerometer, NHANES 2011-2014

Authors:

• Christopher Odoom
• John Staudenmayer
• Additional coauthors to be added

Affiliation:

• Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA

Funding:

This study was funded by the National Institutes of Health (NIH 5R01HL1685355-02).

Repository Contents

R/
  render_report.R
  workflow_figure.R
data/
  self-sleep-2011-12.xpt
  self-sleep-2013-14.xpt
  top_level_data_1h_epoch/
reports/
  source/final_analysis.Rmd
  rendered/
outputs/final_analysis/
figures/final_analysis/

Main Report

The main analysis is:

reports/source/final_analysis.Rmd

It produces the rendered report in:

reports/rendered/

and writes final analysis products to:

outputs/final_analysis/
figures/final_analysis/

Data

The final epoch-level and participant-level analysis datasets are loaded from the wristsed R data package.

The package is a data product of this paper. It provides the cleaned NHANES 2011-2014 wrist accelerometer sedentary-time datasets used by the analysis, including the participant-level estimates of waking sedentary time.

Install the package from GitHub with:

# install.packages("remotes")
remotes::install_github("codoom1/wristsed")

This repository includes only the local files directly used by the report:

data/self-sleep-2011-12.xpt
data/self-sleep-2013-14.xpt
data/top_level_data_1h_epoch/

The top_level_data_1h_epoch/ files build the workflow figure.

Reproduce

From the repository root:

Rscript -e "renv::restore()"
Rscript R/render_report.R html
Rscript R/render_report.R pdf

Check the environment:

Rscript -e "renv::status()"

renv::status() should report no issues.

Outputs

Open the rendered report here:

reports/rendered/final_analysis.html
reports/rendered/final_analysis.pdf

Final tables, results, cutoff files, QC files, and derived participant data are under:

outputs/final_analysis/

Final figure files are under:

figures/final_analysis/

Citation

Odoom C, Staudenmayer J, additional coauthors to be added. Sedentary Behavior in the United States Measured by Accelerometer, NHANES 2011-2014. Manuscript in preparation.