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

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

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