Project Skeleton

A basic repo template (directory structure) to be use as starting point for new projects.

Structure

00-Information

Proposals, prompts, outlines, ... anything relevant to the conception of the project.

01-Data

Data in downloaded formats are "raw" (e.g., .xlsx, .dat, .csv, ...). We import and store data in R formats (e.g., .rds, .rdata) during "processing". Data cleaning and recoding finalize "analytic" datasets. Note: generally, "00-" prefix means don't modify or rewrite the files within.

Sub-directories
- 00-Raw-Data
- 01-Processed-Data
- 02-Analytic-Data

02-Scripts

Envisioned as a linear path from raw data management to final figure creation. Playground to catch everything incomplete; data wrangling to transition through data directories; helper functions to hold project specific functions or those oriented to external programs; visualization is obvious; analysis to fit models, calculate stats, general computation/programming. Each has its own typical set of script types.

Sub-directories and typical scripts
- 00-Playground
  - exploratory code dump, in-progress scripts, under construction, placeholder for other scripts
- 01-Data-Wrangling
  - download_Data_* : scripts to automate the data download from online
  - process_Data_* : scripts to process raw data
  - prep_Files_* : scripts to write files for external program use
  - process_Results_* : scripts to process results from external program analyses
- 02-Helper-Functions
  - repeated, modular, specific, useful code
  - run_Program_* : scripts to automate external programs
- 03-Visualization
  - plot_* : pretty self-explanatory, fundamental units to generate_Figure scripts
  - generate_Figure_* : scripts to create high-level figures, plots, images, interactive visualizations
  - generate_Table_* : scripts to create tables
- 04-Analysis
  - analyze_* : scripts to run analyses within R

03-Output

Store the goodies to show everyone else.

Sub-directories
- 01-Tables
- 02-Figures
- 03-Non-Static

04-Report

Sub-directories
- 01-Notebook (detailed reports, write-ups, long-winded, process-oriented)
  - reproducibility_notebook.RMD : quasi-stream-of-thought writing, deeply woven web of scripts and analytical directions
- 02-Presentation (slide decks)
- 03-Manuscript (polished for publication)