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copilot review updates

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Mike-Hanna 2025-10-23 13:15:44 -04:00
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instructions/r.instructions.md
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--- ---
description: "R language and document formats (R, Rmd, Quarto): coding standards and Copilot guidance for idiomatic, safe, and consistent code generation." description: 'R language and document formats (R, Rmd, Quarto): coding standards and Copilot guidance for idiomatic, safe, and consistent code generation.'
applyTo: "**/*.{R,r,Rmd,rmd,qmd}" applyTo: '**/*.{R,r,Rmd,rmd,qmd}'
--- ---
# R Programming Language Instructions # R Programming Language Instructions
@ -13,8 +13,7 @@ Help GitHub Copilot generate idiomatic, safe, and maintainable R code across pro
- **Match the project’s style.** If the file shows a preference (tidyverse vs. base R, `%>%` vs. `|>`), follow it. - **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. - **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()`. - **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.
In project code, using `library()` is acceptable when that’s the repo norm.
- **Naming:** `lower_snake_case` for objects/files; avoid dots in names. - **Naming:** `lower_snake_case` for objects/files; avoid dots in names.
- **Side effects:** Never call `setwd()`; prefer project-relative paths (e.g., `here::here()`). - **Side effects:** Never call `setwd()`; prefer project-relative paths (e.g., `here::here()`).
- **Reproducibility:** Set seeds locally around stochastic operations using `withr::with_seed()`. - **Reproducibility:** Set seeds locally around stochastic operations using `withr::with_seed()`.
@ -48,7 +47,7 @@ In project code, using `library()` is acceptable when that’s the repo norm.
## Data Wrangling & I/O ## Data Wrangling & I/O
- **Data frames:** prefer tibbles in tidyverse-heavy files; otherwise base `data.frame()` is fine. - **Data frames:** prefer tibbles in tidyverse-heavy files; otherwise base `data.frame()` is fine.
- **Iteration:** use `purrr` in tidyverse code. In base-style code, prefer type-stable, vectorized patterns such as `vapply()` - **Iteration:** use `purrr` in tidyverse code. In base-style code, prefer type-stable, vectorized patterns such as `vapply()`
(for atomic outputs) or `Map()` (for elementwise operations) instead of explicit `for` loops when they improve clarity or performance. (for atomic outputs) or `Map()` (for elementwise operations) instead of explicit `for` loops when they improve clarity or performance.
- **Strings & Dates:** use `stringr`/`lubridate` where already present; otherwise use clear base helpers (e.g., `nchar()`, `substr()`, `as.Date()` with explicit format). - **Strings & Dates:** use `stringr`/`lubridate` where already present; otherwise use clear base helpers (e.g., `nchar()`, `substr()`, `as.Date()` with explicit format).
- **I/O:** prefer explicit, typed readers (e.g., `readr::read_csv()`); make parsing assumptions explicit. - **I/O:** prefer explicit, typed readers (e.g., `readr::read_csv()`); make parsing assumptions explicit.
@ -87,8 +86,7 @@ In project code, using `library()` is acceptable when that’s the repo norm.
## Copilot-Specific Guidance ## Copilot-Specific Guidance
- If the current file uses tidyverse, **suggest tidyverse-first patterns** (e.g., `dplyr::across()` instead of superseded verbs). - If the current file uses tidyverse, **suggest tidyverse-first patterns** (e.g., `dplyr::across()` instead of superseded verbs). If base-R style is present, **use base idioms**.
If base-R style is present, **use base idioms**.
- Qualify non-base calls in suggestions (e.g., `dplyr::mutate()`). - Qualify non-base calls in suggestions (e.g., `dplyr::mutate()`).
- Suggest vectorized or tidy solutions over loops when idiomatic. - Suggest vectorized or tidy solutions over loops when idiomatic.
- Prefer small helper functions over long pipelines. - Prefer small helper functions over long pipelines.
@ -106,7 +104,7 @@ scores$z <- vapply(scores$x, safe_log, numeric(1))
# Tidyverse variant (if this file uses tidyverse) # Tidyverse variant (if this file uses tidyverse)
result <- tibble::tibble(id = 1:5, x = c(1, 3, 2, 5, 4)) |> result <- tibble::tibble(id = 1:5, x = c(1, 3, 2, 5, 4)) |>
dplyr::mutate(z = purrr::possibly(log, otherwise = NA_real_)(x)) |> dplyr::mutate(z = purrr::map_dbl(x, purrr::possibly(log, otherwise = NA_real_))) |>
dplyr::filter(z > 0) dplyr::filter(z > 0)
# Example reusable helper with roxygen2 doc # Example reusable helper with roxygen2 doc