R language and document formats (R, Rmd, Quarto): coding standards and Copilot...

# R Programming Language Instructions

## Purpose

Help GitHub Copilot generate idiomatic, safe, and maintainable R code across projects.

## Core Conventions

- **Match the project’s style.** If the file shows a preference (tidyverse vs. base R, `%>%` vs. `|>`), follow it.
- **Prefer clear, vectorized code.** Keep functions small and avoid hidden side effects.
- **Qualify non-base functions in examples/snippets**, e.g., `dplyr::mutate()`, `stringr::str_detect()`. In project code, using `library()` is acceptable when that’s the repo norm.
- **Naming:** `lower_snake_case` for objects/files; avoid dots in names.
- **Side effects:** Never call `setwd()`; prefer project-relative paths (e.g., `here::here()`).
- **Reproducibility:** Set seeds locally around stochastic operations using `withr::with_seed()`.
- **Validation:** Validate and constrain user inputs; use typed checks and allowlists where possible.
- **Safety:** Avoid `eval(parse())`, unvalidated shell calls, and unparameterized SQL.

### Pipe Operators

- **Native pipe `|>` (R ≥ 4.1.0):** Prefer in R ≥ 4.1 (no extra dependency).
- **Magrittr pipe `%>%`:** Continue using in projects already committed to magrittr or when you need features like `.`, `%T>%`, or `%$%`.
- **Be consistent:** Don't mix `|>` and `%>%` within the same script unless there's a clear technical reason.

## Performance Considerations