├── .gitignore          <- Lists files to be ignored in syncing between local and remote.
├── LICENSE             <- Describes license to the contents of this repo.
├── README.md           <- Describes the project and orchestration (how to run)
│
├── data
│   ├── raw             <- The original, immutable data dump.
│   │   └── <experiment>
│   │       └── <conditions/replicate>
│   │           └── <date as YYYY-MM-DD>
│   ├── external        <- Data from third party sources (e.g., US Census).
│   │   └── <provider>
│   │       └── <date as YYYY-MM-DD>
│   ├── intermediate       <- Intermediate data that has been standardized, formatted, deduped, etc.
│   │   └── <experiment>
│   │       └── <conditions/replicate>
│   │           └── <date as YYYY-MM-DD>
│   ├── extracted       <- Tabular data extracted from conformed image data.
│   │   └── <experiment>
│   │       └── <conditions/replicate>
│   │           └── <date as YYYY-MM-DD>
│   └── tidy            <- The final, canonical datasets for analysis. Includes engineered features.
│       └── <experiment>
│
├── code
│   ├── data-processing <- Code to process data from raw all the way to tidy.
│   │   └── <experiment>
│   ├── draft-analyses  <- Code that operates on tidy data for draft data analytics and visualizations.
│   └── final-analyses  <- Code that operates on tidy data to produce text, figures and tables as they appear in pubilcations.
│
├── output
│   ├── draft           <- Tables and figures from the draft analytics
│   │   └── <experiment>
│   └── final           <- Tables and figures from the final analytics
│
├── docs                <- Data dictionaries, manuals, and all other explanatory materials.
│
├── publication                      
│   └── journal                      <- Journal that this was submitted to
│       └── submission-1_YYYY-MM-DD  <- All materials of submission 1
│           ├── docs                 <- All documents for submission
│           ├── figures              <- All figures for submission
│           └── tables               <- All tables for submission
│
├── .github
│   ├── linters         <- Configuration files for all linters being used
│   └── workflows       <- GitHub Actions workflows
│
├── Dockerfile          <- Use docker build to build Docker container based on this file
├── deps.R              <- Import packages not used elsewhere to help renv
├── renv.lock           <- Lockfile with all dependencies managed by renv
└── renv                <- Package dependency management directory with renv

├── Title
│   ├── Inputs          <- Define the input sources.
│   └── Outputs         <- Define the outputs.
│
├── Setup
│   ├── Import          <- Import modules.
│   ├── Parameters      <- Input parameters (e.g., data definitions)
│   ├── Configs         <- Input any configurations (e.g., source data, % sampled).
│   └── Functions       <- Define all functions.
│
├── Read
│   ├── Import          <- Import data.
│   └── Conform         <- Conform data to a format appropriate for analysis.
│
├── Compute
│   └── Compute - <Analysis type>   <- Compute descriptive statistics, visualize, analyze.
│       └── <Analysis subtype>      <- Analysis subtype (if applicable; e.g., histograms).
│
├── Write
│   ├── Conform         <- Conform data to a format appropriate for storage.
│   └── Export          <- Write/push/sink data to a storage service.
│
├── Reproducibility
│   ├── Linting and styling
│   ├── Dependency management
│   └── Containerization
│
├── Documentation
    ├── Session info
    └── References