R Guide

R Guide

Applies to: R 4.1+, Statistical Computing, Data Analysis, R Packages, Shiny Apps

Core Principles

1. Tidyverse First: Use tidyverse conventions for data manipulation, visualization, and functional programming; fall back to base R only when performance demands it
2. Vectorize Everything: Prefer vectorized operations and purrr::map() over explicit for loops; R is optimized for vector operations
3. Reproducibility: Every analysis must be reproducible -- use renv for dependency management, set.seed() for stochastic operations, and R Markdown/Quarto for literate programming
4. Functional Style: Write pure functions with no side effects; avoid modifying global state or relying on .GlobalEnv
5. Explicit Over Implicit: No reliance on partial matching, implicit type coercion, or positional argument passing for non-trivial functions

Guardrails

Version & Dependencies

• Target R 4.1+ (native pipe |>, lambda shorthand \(x))
• Manage dependencies with renv -- always commit renv.lock
• For packages, declare all dependencies in DESCRIPTION (Imports:, Suggests:)
• Pin CRAN snapshot dates in renv for full reproducibility
• Audit new dependencies: check CRAN status, reverse dependencies, license (GPL compatibility)

Code Style

• Follow the tidyverse style guide
• Run styler::style_pkg() and lintr::lint_package() before every commit
• Naming: snake_case for functions/variables, PascalCase for R6/S4 classes
• Max line length: 80 characters
• Use <- for assignment (not = outside function arguments)
• Explicit library() at top of scripts; never use require()
• Always use TRUE/FALSE (never T/F -- they can be overwritten)
• No attach() or setwd() -- use here::here() for project-relative paths

Vectorization

• Prefer vectorized operations: x * 2 not for (i in seq_along(x)) x[i] * 2
• Use dplyr::mutate() / dplyr::summarise() for column-wise transformations
• Use purrr::map() family for list iteration (map_dbl(), map_chr(), map_dfr())
• Use dplyr::across() for applying functions to multiple columns
• Reserve for loops for side effects only (writing files, API calls)
• Use vapply() over sapply() when base R is required (explicit return type)

Error Handling

• Use rlang::abort() / cli::cli_abort() over stop() for structured conditions
• Validate inputs at the start of every exported function
• Use stopifnot() or rlang::arg_match() for argument validation
• Never use try() -- always tryCatch() or purrr::safely()

validate_dataframe <- function(df, required_cols) {
  if (!is.data.frame(df)) {
    cli::cli_abort("{.arg df} must be a data frame, not {.obj_type_friendly {df}}.")
  }
  missing_cols <- setdiff(required_cols, names(df))
  if (length(missing_cols) > 0) {
    cli::cli_abort(
      "Missing required column{?s}: {.field {missing_cols}}.",
      class = "validation_error"
    )
  }
  invisible(df)
}

Reproducibility

• Always use set.seed() before stochastic operations; document the seed
• Use renv::snapshot() after adding or updating packages
• Never use absolute paths -- use here::here() for project-relative paths
• Use R Markdown (.Rmd) or Quarto (.qmd) for analysis reports
• Include sessioninfo::session_info() at the end of reports

Project Structure

mypackage/                          myanalysis/
├── R/             # Source files   ├── R/             # Reusable functions
│   ├── data-clean.R                ├── analysis/      # Rmd/Quarto (numbered)
│   └── utils.R                     │   ├── 01-exploration.Rmd
├── tests/                          │   └── 02-modeling.qmd
│   ├── testthat.R  # Runner        ├── data/
│   └── testthat/                   │   ├── raw/       # Immutable input
│       └── test-data-clean.R       │   └── processed/ # Generated output
├── man/            # roxygen2      ├── output/        # Figures, reports
├── vignettes/                      ├── tests/testthat/
├── data-raw/       # Data scripts  ├── renv.lock
├── DESCRIPTION                     └── README.md
├── NAMESPACE       # roxygen2
├── renv.lock
└── README.md

• Use roxygen2 for all docs; never edit man/ or NAMESPACE by hand
• Raw data is immutable -- store in data/raw/, process into data/processed/

Key Patterns

Tidyverse Pipe Chains

# Prefer native pipe |> (R 4.1+) over magrittr %>%
result <- raw_data |>
  dplyr::filter(year >= 2020, !is.na(revenue)) |>
  dplyr::mutate(
    revenue_m = revenue / 1e6,
    growth = (revenue - dplyr::lag(revenue)) / dplyr::lag(revenue)
  ) |>
  dplyr::summarise(
    mean_revenue = mean(revenue_m, na.rm = TRUE),
    .by = region
  )

Tidy Evaluation

# Use {{ }} (embrace) for column names passed as arguments
summarise_by <- function(df, group_col, value_col) {
  df |>
    dplyr::summarise(
      mean_val = mean({{ value_col }}, na.rm = TRUE),
      n = dplyr::n(),
      .by = {{ group_col }}
    )
}

# Use .data pronoun for string column references
filter_column <- function(df, col_name, threshold) {
  df |> dplyr::filter(.data[[col_name]] > threshold)
}

# Use across() for multiple columns
standardize_numeric <- function(df) {
  df |>
    dplyr::mutate(dplyr::across(
      where(is.numeric),
      \(x) (x - mean(x, na.rm = TRUE)) / sd(x, na.rm = TRUE)
    ))
}

ggplot2 Grammar of Graphics

plot_distribution <- function(df, x_col, fill_col = NULL) {
  ggplot2::ggplot(df, ggplot2::aes(x = {{ x_col }})) +
    ggplot2::geom_histogram(ggplot2::aes(fill = {{ fill_col }}), bins = 30, alpha = 0.7) +
    ggplot2::labs(title = "Distribution", x = NULL, y = "Count") +
    ggplot2::theme_minimal(base_size = 14)
}

Functional Programming with purrr

# Type-stable map variants -- read and combine CSV files
results <- purrr::map_dfr(file_paths, \(path) {
  readr::read_csv(path, show_col_types = FALSE) |>
    dplyr::mutate(source_file = basename(path))
})

# Safe execution -- capture errors without stopping
safe_read <- purrr::safely(readr::read_csv)
reads <- purrr::map(file_paths, safe_read)
successes <- purrr::map(purrr::keep(reads, \(x) is.null(x$error)), "result")

Testing

Standards

• Use testthat 3rd edition (Config/testthat/edition: 3 in DESCRIPTION)
• Test files: test-*.R (mirror source: data-clean.R -> test-data-clean.R)
• Test names describe behavior: test_that("filter_active removes inactive users", ...)
• Coverage target: >80% for business logic, >60% overall (measured with covr)
• Use snapshot tests (expect_snapshot()) for complex output (plots, printed tables)
• No test interdependencies -- each test_that() block is self-contained
• Use withr::local_*() for temporary state changes (env vars, options, files)

testthat Examples

test_that("summarise_by computes correct group means", {
  df <- tibble::tibble(
    region = c("east", "east", "west", "west"),
    revenue = c(100, 200, 300, 400)
  )
  result <- summarise_by(df, region, revenue)
  expect_equal(nrow(result), 2)
  expect_equal(result$mean_val[result$region == "east"], 150)
})

test_that("validate_dataframe errors on missing columns", {
  df <- tibble::tibble(a = 1, b = 2)
  expect_error(validate_dataframe(df, c("a", "c")), class = "validation_error")
})

Tooling

Essential Commands

Rscript -e 'styler::style_pkg()'        # Format package code
Rscript -e 'lintr::lint_package()'       # Lint package
Rscript -e 'devtools::test()'            # Run tests
Rscript -e 'covr::package_coverage()'    # Coverage report
Rscript -e 'devtools::check()'           # Full R CMD check
Rscript -e 'renv::snapshot()'            # Lock dependencies
Rscript -e 'devtools::document()'        # Rebuild roxygen2 docs
quarto render analysis/report.qmd        # Render Quarto document

References

For detailed patterns and examples, see:

• references/patterns.md -- dplyr pipelines, ggplot2 recipes, purrr functional patterns

External References

• Tidyverse Style Guide
• R for Data Science (2e)
• Advanced R (2e)
• R Packages (2e)
• Tidy Evaluation
• testthat 3e Documentation
• ggplot2 Documentation
• renv Documentation
• Quarto Guide
• lintr Documentation