[Project Name]

Disease / Program: [e.g., Gonorrhea | HIV | Early Syphilis | Chlamydia]
Jurisdiction: [e.g., State Health Department — Division of STD Prevention]
Analyst: [Name]
Created: [YYYY-MM-DD]
Last updated: [YYYY-MM-DD]

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Purpose

[One paragraph describing the purpose of this analysis. What question does it answer? What decision or report will it inform?]

Data Sources

Source	File	Date Received	Notes
[e.g., NNDSS extract]	02_raw_data/nndss_2024.csv	[YYYY-MM-DD]	Annual case data
[e.g., Census population]	02_raw_data/pop_2024.csv	[YYYY-MM-DD]	ACS 5-year estimates

How to Run

Ensure you have R ≥ 4.4 installed. This project uses {renv} for reproducible package management — see "Setup" below.

Run scripts in numbered order from the project root (i.e., with this .Rproj file open in RStudio):

Script	Purpose
scripts/01_ingest.R	Read raw data; validate; save to 03_cleaned_data/
scripts/02_clean.R	Recode variables; handle missing values; apply date logic
scripts/03_analyse.R	Compute rates, proportions, and summary tables
scripts/04_visualise.R	Produce figures; save to 05_output_figures/
scripts/05_report.qmd	Render final report to 06_output_docs/

# Run from the R console (project must be open):
source(here::here("scripts", "01_ingest.R"))
source(here::here("scripts", "02_clean.R"))
# ... etc

Setup

This project uses {renv} to manage package versions reproducibly.

First time on this machine:

renv::init()

Cloning an existing project:

renv::restore()

After setup, all project functions (in R/) are automatically available when you open the .Rproj file. Individual scripts declare their package dependencies with library() calls.

Directory Structure

project_name/
├── project_name.Rproj       ← open this first
├── README.md
├── TODO.md
├── 01_documents/            ← protocols, data dictionaries, background
├── 02_raw_data/             ← source data — NEVER MODIFY
├── 03_cleaned_data/           ← cleaned data ready for analysis
├── 04_output_data/          ← summary tables and intermediate results
├── 05_output_figures/       ← saved plots and maps
├── 06_output_docs/          ← rendered reports (HTML, Word, PDF)
├── R/                       ← reusable helper functions (sourced by scripts)
└── scripts/                 ← numbered analysis scripts and report template

Notes

[Important caveats, known data quality issues, suppression decisions, or methodological choices made during this analysis.]