R Packages. 2nd Edition

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• Preface
  • Welcome!
  • Introduction
    • Philosophy
    • In This Book
    • Whats Not Here
  • Conventions Used in This Book
  • Colophon
  • OReilly Online Learning
  • How to Contact Us
  • Acknowledgments
• I. Getting Started
  • 1. The Whole Game
    • Load devtools and Friends
    • Toy Package: regexcite
    • Preview the Finished Product
    • create_package()
    • use_git()
    • Write the First Function
    • use_r()
    • load_all()
      • Commit strsplit1()
    • check()
    • Edit DESCRIPTION
    • use_mit_license()
    • document()
      • NAMESPACE Changes
    • check() Again
    • install()
    • use_testthat()
    • use_package()
    • use_github()
    • use_readme_rmd()
    • The End: check() and install()
    • Review
  • 2. System Setup
    • devtools, usethis, and You
      • Personal Startup Configuration
    • R Build Toolchain
      • Windows
      • macOS
      • Linux
    • Verify System Prep
  • 3. Package Structure and State
    • Package States
    • Source Package
    • Bundled Package
      • .Rbuildignore
    • Binary Package
    • Installed Package
    • In-Memory Package
    • Package Libraries
  • 4. Fundamental Development Workflows
    • Create a Package
      • Survey the Existing Landscape
      • Name Your Package
        • Formal requirements
        • Things to consider
        • Use the available package
      • Package Creation
      • Where Should You create_package()?
    • RStudio Projects
      • Benefits of RStudio Projects
      • How to Get an RStudio Project
      • What Makes an RStudio Project?
      • How to Launch an RStudio Project
      • RStudio Project Versus Active usethis Project
    • Working Directory and Filepath Discipline
    • Test Drive with load_all()
      • Benefits of load_all()
      • Other Ways to Call load_all()
    • check() and R CMD check
      • Workflow
      • Background on R CMD check
  • 5. The Package Within
    • Alfa: A Script That Works
    • Bravo: A Better Script That Works
    • Charlie: A Separate File for Helper Functions
    • Delta: A Failed Attempt at Making a Package
    • Echo: A Working Package
    • Foxtrot: Build Time Versus Run Time
    • Golf: Side Effects
    • Concluding Thoughts
      • Script Versus Package
      • Finding the Package Within
      • Package Code Is Different
• II. Package Components
  • 6. R Code
    • Organize Functions Into Files
    • Fast Feedback via load_all()
    • Code Style
    • Understand When Code Is Executed
      • Example: A Path Returned by system.file()
      • Example: Available Colors
      • Example: Aliasing a Function
    • Respect the R Landscape
      • Manage State with withr
      • Restore State with base::on.exit()
      • Isolate Side Effects
      • When You Do Need Side Effects
    • Constant Health Checks
  • 7. Data
    • Exported Data
      • Preserve the Origin Story of Package Data
      • Documenting Datasets
      • Non-ASCII Characters in Data
    • Internal Data
    • Raw Data File
      • Filepaths
      • pkg_example() Path Helpers
    • Internal State
    • Persistent User Data
  • 8. Other Components
    • Other Directories
    • Installed Files
      • Package Citation
    • Configuration Tools
• III. Package Metadata
  • 9. DESCRIPTION
    • The DESCRIPTION File
    • Title and Description: What Does Your Package Do?
    • Author: Who Are You?
    • URL and BugReports
    • The License Field
    • Imports, Suggests, and Friends
      • Minimum Versions
      • Depends and LinkingTo
      • An R Version Gotcha
    • Other Fields
    • Custom Fields
  • 10. Dependencies: Mindset and Background
    • When Should You Take a Dependency?
      • Dependencies Are Not Equal
      • Prefer a Holistic, Balanced, and Quantitative Approach
      • Dependency Thoughts Specific to the tidyverse
      • Whether to Import or Suggest
    • Namespace
      • Motivation
      • The NAMESPACE File
    • Search Path
      • Function Lookup for User Code
      • Function Lookup Inside a Package
    • Attaching Versus Loading
      • Whether to Import or Depend
  • 11. Dependencies: In Practice
    • Confusion About Imports
    • Conventions for This Chapter
    • NAMESPACE Workflow
    • Package Is Listed in Imports
      • In Code Below R/
        • How to not use a package in Imports
      • In Test Code
      • In Examples and Vignettes
    • Package Is Listed in Suggests
      • In Code Below R/
      • In Test Code
      • In Examples and Vignettes
    • Package Is Listed in Depends
      • In Code Below R/ and in Test Code
      • In Examples and Vignettes
    • Package Is a Nonstandard Dependency
      • Depending on the Development Version of a Package
      • Config/Needs/* Field
    • Exports
      • What to Export
      • Re-exporting
    • Imports and Exports Related to S3
  • 12. Licensing
    • Big Picture
    • Code You Write
      • Key Files
      • More Licenses for Code
      • Licenses for Data
      • Relicensing
    • Code Given to You
    • Code You Bundle
      • License Compatibility
      • How to Include
    • Code You Use
• IV. Testing
  • 13. Testing Basics
    • Why Is Formal Testing Worth the Trouble?
    • Introducing testthat
    • Test Mechanics and Workflow
      • Initial Setup
      • Create a Test
      • Run Tests
        • Micro-Iteration
        • Mezzo-Iteration
        • Macro-Iteration
    • Test Organization
    • Expectations
      • Testing for Equality
      • Testing Errors
      • Snapshot Tests
      • Shortcuts for Other Common Patterns
  • 14. Designing Your Test Suite
    • What to Test
      • Test Coverage
    • High-Level Principles for Testing
      • Self-Sufficient Tests
      • Self-Contained Tests
      • Plan for Test Failure
      • Repetition Is OK
      • Remove Tension Between Interactive and Automated Testing
    • Files Relevant to Testing
      • Hiding in Plain Sight: Files Below R/
      • tests/testthat.R
      • testthat Helper Files
      • testthat Setup Files
      • Files Ignored by testthat
      • Storing Test Data
      • Where to Write Files During Testing
  • 15. Advanced Testing Techniques
    • Test Fixtures
      • Create useful_things with a Helper Function
      • Create (and Destroy) a Local useful_thing
      • Store a Concrete useful_thing Persistently
    • Building Your Own Testing Tools
      • Helper Defined Inside a Test
      • Custom Expectations
    • When Testing Gets Hard
      • Skipping a Test
        • testthat::skip()
        • Built-In skip() functions
        • Dangers of skipping
      • Mocking
      • Secrets
    • Special Considerations for CRAN Packages
      • Skip a Test
      • Speed
      • Reproducibility
      • Flaky Tests
      • Process and Filesystem Hygiene
• V. Documentation
  • 16. Function Documentation
    • roxygen2 Basics
      • The Documentation Workflow
      • roxygen2 Comments, Blocks, and Tags
      • Key Markdown Features
    • Title, Description, Details
      • Title
      • Description
      • Details
    • Arguments
      • Multiple Arguments
      • Inheriting Arguments
    • Return Value
    • Examples
      • Contents
      • Leave the World as You Found It
      • Errors
      • Dependencies and Conditional Execution
      • Intermixing Examples and Text
    • Reusing Documentation
      • Multiple Functions in One Topic
      • Inheriting Documentation
      • Child Documents
    • Help Topic for the Package
  • 17. Vignettes
    • Workflow for Writing a Vignette
    • Metadata
    • Advice on Writing Vignettes
      • Diagrams
      • Links
      • Filepaths
      • How Many Vignettes?
      • Scientific Publication
    • Special Considerations for Vignette Code
      • Article Instead of Vignette
    • How Vignettes Are Built and Checked
      • R CMD build and Vignettes
      • R CMD check and Vignettes
  • 18. Other Markdown Files
    • README
      • README.Rmd and README.md
    • NEWS
  • 19. Website
    • Initiate a Site
    • Deployment
    • Now What?
    • Logo
    • Reference Index
      • Rendered Examples
      • Linking
      • Index Organization
    • Vignettes and Articles
      • Linking
      • Index Organization
      • NonVignette Articles
    • Development Mode
• VI. Maintenance and Distribution
  • 20. Software Development Practices
    • Git and GitHub
      • Standard Practice
    • Continuous Integration
      • GitHub Actions
      • R CMD check via GHA
      • Other Uses for GHA
  • 21. Lifecycle
    • Package Evolution
    • Package Version Number
    • Tidyverse Package Version Conventions
    • Backward Compatibility and Breaking Change
    • Major Versus Minor Versus Patch Release
      • Package Version Mechanics
    • Pros and Cons of Breaking Change
    • Lifecycle Stages and Supporting Tools
      • Lifecycle Stages and Badges
      • Deprecating a Function
      • Deprecating an Argument
      • Deprecation Helpers
      • Dealing with Change in a Dependency
      • Superseding a Function
  • 22. Releasing to CRAN
    • Decide the Release Type
    • Initial CRAN Release: Special Considerations
      • CRAN Policies
    • Keeping Up with Change
    • Double R CMD Checking
      • CRAN Check Flavors and Related Services
    • Reverse Dependency Checks
      • Revdeps and Breaking Changes
    • Update Comments for CRAN
    • The Submission Process
    • Failure Modes
    • Celebrating Success
• Index

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