Analysis of Adherence

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ANALYSIS OF ADHERENCE
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This directory contains R scripts, data files, and analysis reports related
to the analysis of adherence.

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FILE OVERVIEW
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DATA FILES
* data.xlsx
  Main subject-level dataset.

* data-fitbit.xlsx
  Dataset with detailed Fitbit-derived measures.

DATA LOADING AND PREPROCESSING
* data.R
  R script for loading and preprocessing the main dataset.

* data-fitbit.R
  R script for loading and preprocessing the detailed Fitbit dataset.

DESCRIPTIVE AND BASELINE ANALYSES
* summary.Rmd
  R Markdown document providing a basic description of the datasets.

* baseline.Rmd
  R Markdown document with baseline characteristics and missing-value
  analysis, including evaluation and imputation of missing values in SWL
  (new variable SWLlm.predicted).

* baseline-by-burst.Rmd
  R Markdown document with baseline characteristics stratified by burst
  number.

MODELING AND VARIABLE IMPORTANCE
* importance.Rmd
  R Markdown analysis template for evaluating variable importance using
  stepwise regression and random forest models.

PROJECT CONFIGURATION AND BUILD SYSTEM
* Makefile.R
  Project definition for the rmake package; generates the GNU Makefile.

* Makefile
  File dependencies and compilation commands used by GNU Make to generate
  all project results.

* Rproject.Rproj
  RStudio project file.

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REQUIREMENTS
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1) INSTALL REQUIRED R PACKAGES

Run the following commands in R:

  install.packages(c(
    "tidyverse", "knitr", "rmake", "caret", "randomForest",
    "fastDummies", "broom", "devtools"
  ))
  devtools::install_github("beerda/hammer")
  devtools::install_github("beerda/mbrtools")

2) GENERATE PROJECT ANALYSES

Run the analysis pipeline using rmake:

  make()

This command generates all results defined in the project Makefile.
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