R Packages Organize Test Document and Share Your Code 2nd Edition by Hadley Wickham, Jennifer Bryan ISBNN 9781098134938 1098134931

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Product details:

ISBN 10: 1098134931
ISBN 13: 9781098134938
Author: Hadley Wickham, Jennifer Bryan

R Packages Organize Test Document and Share Your Code 2nd Edition Table of contents:

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

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/

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

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

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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Tags: Hadley Wickham, Jennifer Bryan, R Packages, Organize, Test, Document