style-guide

name	style-guide
description	R style guide: directory structure, .qmd runner, targets, naming, function docs. Use when writing or refactoring R code, or reviewing a diff for style consistency.

Project Style Guide: R Research Projects

Conventions for R-based academic research projects. Adopt what fits; adapt what doesn't.

---

Directory structure

project_name/
├── code/
│   ├── runner.qmd                # single entry point
│   ├── _targets.R                # pipeline DAG (if using targets)
│   ├── scripts/                  # all .R files: functions only, no loose code
│   │   ├── constants.R           # global constants and configuration
│   │   ├── tools.R               # shared helper functions
│   │   ├── groundhog_custom.R    # package management wrapper
│   │   ├── table_*.R             # one file per table (or family)
│   │   └── figure_*.R            # one file per figure (or family)
│   ├── tests/                    # validation scripts
│   └── deprecated/               # old code kept for reference, never sourced
├── data/                         # raw data; never modified
├── tables/                       # generated .tex / .csv
├── figures/                      # generated .pdf / .png
├── temp/                         # ephemeral; gitignored
├── writing/                      # manuscript + bibliography
└── for_claude/                   # AI instructions and planning docs

Key principles

• One runner to rule them all. The whole pipeline runs from a single .qmd file. Press "Run All" → reproduce every output.
• No ad hoc script execution. Don't run individual .R files or Rscript -e "..." to produce outputs. Always go through runner.qmd. Ad hoc execution bypasses version pinning and dependency tracking.
• Raw data is read-only. Never modify files in data/.
• Functions live in scripts/. No loose procedural code.
• Outputs are disposable. Anything in tables/ and figures/ is regenerable. Nothing hand-edited lives here.
• Deprecated code goes to deprecated/, not the trash -- searchable but clearly inactive.

---

The runner file (.qmd)

Why .qmd and not .R? A Quarto file auto-sets its working directory to its own location. Relative paths resolve correctly without .Rproj or here::here(). A plain .R script's working directory depends on how RStudio or the terminal was launched -- a common "works on my machine" failure.

We deliberately avoid .Rproj files (invasive: they create .Rproj.user/, change RStudio behaviour, encourage IDE-specific assumptions).

Minimal pattern:

# Setup
```{r setup}
source("scripts/constants.R")
source("scripts/groundhog_custom.R")
pkgs <- c("tidyverse", "haven", "fixest", "modelsummary", ...)
groundhog_custom(pkgs, "YYYY-MM-DD", update = TRUE)

Pipeline

targets::tar_make()

Conventions:
- **Chunk names match function names.** If a chunk calls `table_balance()`, the chunk is named `table_balance`.
- **One function call per chunk** where possible.
- **The runner reads like a table of contents** for the paper's results.

---

## `{targets}` pipeline

For projects with multiple data sources, slow steps, or complex dependency chains, `{targets}` replaces direct function calls with a dependency-aware DAG.

`_targets.R` sits beside `runner.qmd`, sources all scripts, sets the package context, defines targets:

```r
library(targets)
lapply(list.files("scripts", pattern = "\\.R$", full.names = TRUE), source)
tar_option_set(packages = c("tidyverse", "fixest", "modelsummary"))

list(
  tar_target(file_data, constants$data_path, format = "file"),
  tar_target(dat, clean_data(haven::read_dta(file_data))),
  tar_target(main_table, table_main(dat)),
  tar_target(main_figure, figure_main(dat))
)

Key conventions:

• Each target calls exactly one function. That function handles its own output side-effect (.tex / .pdf to disk) and returns an R object for downstream targets.
• format = "file" for raw data so the pipeline detects when source files change.
• Keep the package list in sync between groundhog_custom() in the runner and tar_option_set(packages = ...).
• Don't commit _targets/objects/ -- regenerable and can be large.

For simple projects with a single data source and fast computations, skip {targets} and use direct function calls in the runner.

---

Constants (constants.R)

Project-wide configuration in a single named list. Sourced first; available everywhere:

constants <- list(
  outtab = "../tables/",
  outfig = "../figures/",
  data_main = "../data/source_a/main_data.dta",
  bandwidth = 20,
  outcomes  = c("outcome_1", "outcome_2"),
  cmap = c("treatment" = "Treatment", "(Intercept)" = "Intercept")
)

Use constants$outtab everywhere. Namespaced and discoverable. Don't put values used by only one function in constants; keep those local.

---

Scripts (tools.R, table_*.R, figure_*.R)

• tools.R -- helpers used by more than one script. If only one script uses it, leave it there. Functions migrate to tools.R when a second script needs them.
• table_*.R -- each file defines one function (or small family) producing one or more tables. File name matches the function (table_main.R → table_main()). Output: tab_main.tex.
• figure_*.R -- same pattern. Function saves to disk and returns the plot object.

Pick one estimation package per project and use it consistently (fixest::feols() for panel/IV/clustered SEs, estimatr::lm_robust() for cross-sectional experiments). Use modelsummary() for all .tex output. Use ggsave() to PDF for figures.

---

Package management (groundhog_custom.R)

We use a groundhog wrapper that pins package versions and auto-increments the snapshot date in 6-month windows. Three modes: fallback = TRUE (dev), fallback = FALSE, update = TRUE (production), fallback = FALSE, update = FALSE (archival, locks the original date for final submission).

The wrapper definition itself lives in scripts/groundhog_custom.R.

---

Naming conventions

Thing	Convention	Example
Variables	snake_case	vote_share, turnout
Functions	snake_case, prefixed by output type	table_main(), figure_pooled()
Script files	match the primary function	table_main.R
Output files	tab_ or fig_ prefix	tab_main.tex, fig_pooled.pdf
Constants	constants$<name>	constants$bandwidth
Target names	snake_case, descriptive	dat_cleaned, models_main

---

Function documentation

Every function gets a header comment:

my_function <- function(foo, bar) {
  # brief description of what the function does
  # inputs:
  #   foo: description
  #   bar: description
  # outputs:
  #   description of what is returned or saved to disk
  ...
}

Lightweight -- not roxygen. State inputs, outputs, purpose.

---

Sibling skills

• sweep skill -- full pipeline rebuild from scratch to verify reproducibility.
• maintenance skill -- testing, linting, refactoring, documentation passes.

Both require a clean git state before starting.