primarycensored-paper

A repository for the paper "Modelling delays with primary Event Censored Distributions", which describes methods for handling double interval censored data in epidemiological delay distribution estimation.

Repository Structure

• paper/: Contains the Quarto document for the manuscript
  • main.qmd: Main manuscript
  • si.qmd: Supplementary information
  • reference.bib: Bibliography
• _targets.Rmd: Reproducible analysis pipeline (see below)
• R/: Analysis functions used in the targets workflow
• scripts/: R scripts for task automation and development
• data/: Data directory for raw, processed, and results
• figures/: Generated figures from the analysis

Analysis Pipeline

The analysis uses the targets R package for reproducibility. The pipeline is defined in _targets.Rmd.

Getting Started

Install Task from https://taskfile.dev/installation/, then run:

# Complete workflow (sets up dependencies + runs analysis + renders manuscript)
task

# Or step by step:
task restore    # Restore R packages from lockfile
task render     # Render _targets.Rmd to create pipeline
task run        # Execute the targets pipeline
task manuscript # Render manuscript to PDF and HTML

The default task command automatically handles the complete analysis pipeline. Run task help to see all available commands.

For configuration options and development workflows, see docs/DEVELOPMENT.md.