ukb_repeat_accelerometry/main.R at main · OxWearables/ukb_repeat_accelerometry · GitHub

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# ============================================================================
# Complete analysis pipeline for the UK Biobank repeat accelerometry sub-study
# ============================================================================

# Clean workspace and load configuration
rm(list = ls())

source(here::here("config.R"))

# Create output directories
dir.create(here::here("output/tables"), recursive = TRUE)
dir.create(here::here("output/figures"), recursive = TRUE)

# ===========================================================================
# Stage 1: Dataset preparation
# ===========================================================================

message("========== Loading and processing main accelerometer data...")
source(here::here("R", "1-prep", "01_prepare_main_phenotypes.R"))

message("========== Loading and processing repeat accelerometer data...")
source(here::here("R", "1-prep", "02_prepare_repeat_phenotypes.R"))

message("========== Applying quality control and exclusion criteria...")
source(here::here("R", "1-prep", "03_apply_exclusions.R"))

message("========== Reshaping and merging main with repeat measurements...")
source(here::here("R", "1-prep", "04_merge_main_repeat.R"))

message("========== Assembling final analysis dataset...")
source(here::here("R", "1-prep", "05_prepare_complete_dataset.R"))

# ===========================================================================
# Stage 2: Reproducibility analysis
# ===========================================================================

message("========== Running reproducibility and descriptive analysis...")
rmarkdown::render(
  here::here("R", "2-analysis", "01_reproducibility_analysis.Rmd"),
  output_dir = here::here("output"),
  quiet = TRUE
)

# ===========================================================================
# Stage 3: Epidemiological analysis
# ===========================================================================

message("========== Running epidemiological analysis...")
rmarkdown::render(
  here::here("R", "2-analysis", "02_epidemiological_analysis.Rmd"),
  output_dir = here::here("output"),
  quiet = TRUE
)

message("========== Pipeline finished successfully!")