Project Template

This repository contains a template for my projects.

Folder Structure

• scripts: Scripts that conduct the analysis pipeline, from data collection (if appropriate) through cleaning to analysis

• data: Data files, both raw data and intermediate data files created by the pipeline scripts

• plots: Plots and other figures created by the pipeline scripts

  • Alternative: output if the project creates several tables or other outputs

• R: R files containing utility functions used repeatedly in the analysis pipeline

  • Load in scripts using devtools::load_all('..')
  • Requires valid DESCRIPTION

• paper: Files used to generate the paper

  • paper.qmd containing the paper body
  • _quarto.yml containing some nice typesetting
  • bibfile.yaml file should be placed in the top level, for use by both paper and talk
  • The project makefile should copy/rename figures from plots to paper

• talk: Files used to generate the talk/slides

File Naming

Files in scripts, data, and plots should generally use a sequential naming convention:

• Scripts in scripts should have filenames starting with 01_:

  • 01_scrape.R
  • 02_parse.R
  • 03_eda.R, and so on

• Data and plot files (data and plots) should use a parallel naming convention:

  • 00_ indicates raw data (produced or gathered outside of the pipeline in scripts)
  • 01_ indicates plots and intermediate data files produced by script number 01, and so on

Infrastructure Files

• Makefile should include the following targets:

  • all: pipe, talk, and paper
  • pipe: make the analysis pipeline
  • clean: clean intermediate files from data and plots

• DESCRIPTION: Required for the minimal valid package structure expected by devtools::load_all()

  • See http://www.hep.by/gnu/r-patched/r-exts/R-exts_4.html