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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html#purpose-of-this-book"><i class="fa fa-check"></i>Purpose of this Book</a></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#about-the-author"><i class="fa fa-check"></i>About the Author</a></li>
</ul></li>
<li class="chapter" data-level="1" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>1</b> Introduction</a>
<ul>
<li class="chapter" data-level="1.1" data-path="introduction.html"><a href="introduction.html#why-coding-practices-matter"><i class="fa fa-check"></i><b>1.1</b> Why Coding Practices Matter</a></li>
<li class="chapter" data-level="1.2" data-path="introduction.html"><a href="introduction.html#what-this-book-covers"><i class="fa fa-check"></i><b>1.2</b> What This Book Covers</a></li>
<li class="chapter" data-level="1.3" data-path="introduction.html"><a href="introduction.html#how-to-use-this-book"><i class="fa fa-check"></i><b>1.3</b> How to Use This Book</a></li>
<li class="chapter" data-level="1.4" data-path="introduction.html"><a href="introduction.html#who-this-book-is-for"><i class="fa fa-check"></i><b>1.4</b> Who This Book Is For</a></li>
<li class="chapter" data-level="1.5" data-path="introduction.html"><a href="introduction.html#final-thoughts"><i class="fa fa-check"></i><b>1.5</b> Final Thoughts</a></li>
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<li class="chapter" data-level="2" data-path="naming-conventions.html"><a href="naming-conventions.html"><i class="fa fa-check"></i><b>2</b> Naming Conventions</a>
<ul>
<li class="chapter" data-level="2.1" data-path="naming-conventions.html"><a href="naming-conventions.html#naming-scripts"><i class="fa fa-check"></i><b>2.1</b> Naming Scripts</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="naming-conventions.html"><a href="naming-conventions.html#best-practices-for-script-names"><i class="fa fa-check"></i><b>2.1.1</b> Best Practices for Script Names</a></li>
<li class="chapter" data-level="2.1.2" data-path="naming-conventions.html"><a href="naming-conventions.html#example-script-names"><i class="fa fa-check"></i><b>2.1.2</b> Example Script Names</a></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="naming-conventions.html"><a href="naming-conventions.html#naming-variables"><i class="fa fa-check"></i><b>2.2</b> Naming Variables</a>
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<li class="chapter" data-level="2.2.1" data-path="naming-conventions.html"><a href="naming-conventions.html#guidelines-for-variable-names"><i class="fa fa-check"></i><b>2.2.1</b> Guidelines for Variable Names</a></li>
<li class="chapter" data-level="2.2.2" data-path="naming-conventions.html"><a href="naming-conventions.html#example-variable-names"><i class="fa fa-check"></i><b>2.2.2</b> Example Variable Names</a></li>
</ul></li>
<li class="chapter" data-level="2.3" data-path="naming-conventions.html"><a href="naming-conventions.html#naming-functions"><i class="fa fa-check"></i><b>2.3</b> Naming Functions</a>
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<li class="chapter" data-level="2.3.1" data-path="naming-conventions.html"><a href="naming-conventions.html#best-practices-for-function-names"><i class="fa fa-check"></i><b>2.3.1</b> Best Practices for Function Names</a></li>
<li class="chapter" data-level="2.3.2" data-path="naming-conventions.html"><a href="naming-conventions.html#example-function-names"><i class="fa fa-check"></i><b>2.3.2</b> Example Function Names</a></li>
</ul></li>
<li class="chapter" data-level="2.4" data-path="naming-conventions.html"><a href="naming-conventions.html#consistency-is-key"><i class="fa fa-check"></i><b>2.4</b> Consistency is Key</a></li>
<li class="chapter" data-level="2.5" data-path="naming-conventions.html"><a href="naming-conventions.html#summary"><i class="fa fa-check"></i><b>2.5</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="organising-scripts.html"><a href="organising-scripts.html"><i class="fa fa-check"></i><b>3</b> Organising Scripts</a>
<ul>
<li class="chapter" data-level="3.1" data-path="organising-scripts.html"><a href="organising-scripts.html#structuring-scripts"><i class="fa fa-check"></i><b>3.1</b> Structuring Scripts</a>
<ul>
<li class="chapter" data-level="3.1.1" data-path="organising-scripts.html"><a href="organising-scripts.html#logical-script-structure"><i class="fa fa-check"></i><b>3.1.1</b> Logical Script Structure</a></li>
<li class="chapter" data-level="3.1.2" data-path="organising-scripts.html"><a href="organising-scripts.html#using-functions-for-modularity"><i class="fa fa-check"></i><b>3.1.2</b> Using Functions for Modularity</a></li>
<li class="chapter" data-level="3.1.3" data-path="organising-scripts.html"><a href="organising-scripts.html#script-length"><i class="fa fa-check"></i><b>3.1.3</b> Script Length</a></li>
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<li class="chapter" data-level="3.2" data-path="organising-scripts.html"><a href="organising-scripts.html#organising-files-and-directories"><i class="fa fa-check"></i><b>3.2</b> Organising Files and Directories</a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="organising-scripts.html"><a href="organising-scripts.html#directory-structure"><i class="fa fa-check"></i><b>3.2.1</b> Directory Structure</a></li>
<li class="chapter" data-level="3.2.2" data-path="organising-scripts.html"><a href="organising-scripts.html#data-files"><i class="fa fa-check"></i><b>3.2.2</b> Data Files</a></li>
<li class="chapter" data-level="3.2.3" data-path="organising-scripts.html"><a href="organising-scripts.html#scripts"><i class="fa fa-check"></i><b>3.2.3</b> Scripts</a></li>
<li class="chapter" data-level="3.2.4" data-path="organising-scripts.html"><a href="organising-scripts.html#output-files"><i class="fa fa-check"></i><b>3.2.4</b> Output Files</a></li>
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<li class="chapter" data-level="3.3" data-path="organising-scripts.html"><a href="organising-scripts.html#documentation"><i class="fa fa-check"></i><b>3.3</b> Documentation</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="organising-scripts.html"><a href="organising-scripts.html#readme-files"><i class="fa fa-check"></i><b>3.3.1</b> README Files</a></li>
<li class="chapter" data-level="3.3.2" data-path="organising-scripts.html"><a href="organising-scripts.html#inline-documentation"><i class="fa fa-check"></i><b>3.3.2</b> Inline Documentation</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="organising-scripts.html"><a href="organising-scripts.html#summary-1"><i class="fa fa-check"></i><b>3.4</b> Summary</a></li>
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<li class="chapter" data-level="4" data-path="commenting-code.html"><a href="commenting-code.html"><i class="fa fa-check"></i><b>4</b> Commenting Code</a>
<ul>
<li class="chapter" data-level="4.1" data-path="commenting-code.html"><a href="commenting-code.html#the-purpose-of-comments"><i class="fa fa-check"></i><b>4.1</b> The Purpose of Comments</a>
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<li class="chapter" data-level="4.1.1" data-path="commenting-code.html"><a href="commenting-code.html#why-comment-your-code"><i class="fa fa-check"></i><b>4.1.1</b> Why Comment Your Code?</a></li>
<li class="chapter" data-level="4.1.2" data-path="commenting-code.html"><a href="commenting-code.html#when-to-comment"><i class="fa fa-check"></i><b>4.1.2</b> When to Comment</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="commenting-code.html"><a href="commenting-code.html#best-practices-for-commenting"><i class="fa fa-check"></i><b>4.2</b> Best Practices for Commenting</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="commenting-code.html"><a href="commenting-code.html#writing-clear-and-concise-comments"><i class="fa fa-check"></i><b>4.2.1</b> Writing Clear and Concise Comments</a></li>
<li class="chapter" data-level="4.2.2" data-path="commenting-code.html"><a href="commenting-code.html#comment-placement"><i class="fa fa-check"></i><b>4.2.2</b> Comment Placement</a></li>
<li class="chapter" data-level="4.2.3" data-path="commenting-code.html"><a href="commenting-code.html#consistency-in-commenting"><i class="fa fa-check"></i><b>4.2.3</b> Consistency in Commenting</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="commenting-code.html"><a href="commenting-code.html#common-pitfalls-to-avoid"><i class="fa fa-check"></i><b>4.3</b> Common Pitfalls to Avoid</a>
<ul>
<li class="chapter" data-level="4.3.1" data-path="commenting-code.html"><a href="commenting-code.html#over-commenting"><i class="fa fa-check"></i><b>4.3.1</b> Over-Commenting</a></li>
<li class="chapter" data-level="4.3.2" data-path="commenting-code.html"><a href="commenting-code.html#commenting-out-code"><i class="fa fa-check"></i><b>4.3.2</b> Commenting Out Code</a></li>
<li class="chapter" data-level="4.3.3" data-path="commenting-code.html"><a href="commenting-code.html#vague-or-uninformative-comments"><i class="fa fa-check"></i><b>4.3.3</b> Vague or Uninformative Comments</a></li>
</ul></li>
<li class="chapter" data-level="4.4" data-path="commenting-code.html"><a href="commenting-code.html#advanced-commenting-techniques"><i class="fa fa-check"></i><b>4.4</b> Advanced Commenting Techniques</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="commenting-code.html"><a href="commenting-code.html#using-roxygen2-for-documentation"><i class="fa fa-check"></i><b>4.4.1</b> Using Roxygen2 for Documentation</a></li>
<li class="chapter" data-level="4.4.2" data-path="commenting-code.html"><a href="commenting-code.html#writing-to-do-comments"><i class="fa fa-check"></i><b>4.4.2</b> Writing “To-Do” Comments</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="commenting-code.html"><a href="commenting-code.html#summary-2"><i class="fa fa-check"></i><b>4.5</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html"><i class="fa fa-check"></i><b>5</b> Code Syntax and Spacing</a>
<ul>
<li class="chapter" data-level="5.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#importance-of-consistent-syntax"><i class="fa fa-check"></i><b>5.1</b> Importance of Consistent Syntax</a>
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<li class="chapter" data-level="5.1.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#why-syntax-matters"><i class="fa fa-check"></i><b>5.1.1</b> Why Syntax Matters</a></li>
<li class="chapter" data-level="5.1.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#adopting-a-style-guide"><i class="fa fa-check"></i><b>5.1.2</b> Adopting a Style Guide</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#indentation"><i class="fa fa-check"></i><b>5.2</b> Indentation</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#standard-indentation-practices"><i class="fa fa-check"></i><b>5.2.1</b> Standard Indentation Practices</a></li>
<li class="chapter" data-level="5.2.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#indentation-in-functions"><i class="fa fa-check"></i><b>5.2.2</b> Indentation in Functions</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing"><i class="fa fa-check"></i><b>5.3</b> Spacing</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing-around-operators"><i class="fa fa-check"></i><b>5.3.1</b> Spacing Around Operators</a></li>
<li class="chapter" data-level="5.3.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing-after-commas-and-colons"><i class="fa fa-check"></i><b>5.3.2</b> Spacing After Commas and Colons</a></li>
<li class="chapter" data-level="5.3.3" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing-in-function-calls"><i class="fa fa-check"></i><b>5.3.3</b> Spacing in Function Calls</a></li>
<li class="chapter" data-level="5.3.4" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing-in-conditional-statements"><i class="fa fa-check"></i><b>5.3.4</b> Spacing in Conditional Statements</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#line-breaks"><i class="fa fa-check"></i><b>5.4</b> Line Breaks</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#breaking-long-lines"><i class="fa fa-check"></i><b>5.4.1</b> Breaking Long Lines</a></li>
<li class="chapter" data-level="5.4.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#avoiding-deep-nesting"><i class="fa fa-check"></i><b>5.4.2</b> Avoiding Deep Nesting</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#aligning-code"><i class="fa fa-check"></i><b>5.5</b> Aligning Code</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#aligning-assignments"><i class="fa fa-check"></i><b>5.5.1</b> Aligning Assignments</a></li>
<li class="chapter" data-level="5.5.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#aligning-function-arguments"><i class="fa fa-check"></i><b>5.5.2</b> Aligning Function Arguments</a></li>
</ul></li>
<li class="chapter" data-level="5.6" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#comment-placement-and-spacing"><i class="fa fa-check"></i><b>5.6</b> Comment Placement and Spacing</a>
<ul>
<li class="chapter" data-level="5.6.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#spacing-before-comments"><i class="fa fa-check"></i><b>5.6.1</b> Spacing Before Comments</a></li>
<li class="chapter" data-level="5.6.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#block-comment-formatting"><i class="fa fa-check"></i><b>5.6.2</b> Block Comment Formatting</a></li>
</ul></li>
<li class="chapter" data-level="5.7" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#avoiding-common-pitfalls"><i class="fa fa-check"></i><b>5.7</b> Avoiding Common Pitfalls</a>
<ul>
<li class="chapter" data-level="5.7.1" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#overuse-of-blank-lines"><i class="fa fa-check"></i><b>5.7.1</b> Overuse of Blank Lines</a></li>
<li class="chapter" data-level="5.7.2" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#avoiding-excessive-line-length"><i class="fa fa-check"></i><b>5.7.2</b> Avoiding Excessive Line Length</a></li>
</ul></li>
<li class="chapter" data-level="5.8" data-path="code-syntax-and-spacing.html"><a href="code-syntax-and-spacing.html#summary-3"><i class="fa fa-check"></i><b>5.8</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="writing-functions.html"><a href="writing-functions.html"><i class="fa fa-check"></i><b>6</b> Writing Functions</a>
<ul>
<li class="chapter" data-level="6.1" data-path="writing-functions.html"><a href="writing-functions.html#the-purpose-of-functions"><i class="fa fa-check"></i><b>6.1</b> The Purpose of Functions</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="writing-functions.html"><a href="writing-functions.html#why-write-functions"><i class="fa fa-check"></i><b>6.1.1</b> Why Write Functions?</a></li>
<li class="chapter" data-level="6.1.2" data-path="writing-functions.html"><a href="writing-functions.html#when-to-write-a-function"><i class="fa fa-check"></i><b>6.1.2</b> When to Write a Function</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="writing-functions.html"><a href="writing-functions.html#structure-of-a-function"><i class="fa fa-check"></i><b>6.2</b> Structure of a Function</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="writing-functions.html"><a href="writing-functions.html#basic-function-structure"><i class="fa fa-check"></i><b>6.2.1</b> Basic Function Structure</a></li>
<li class="chapter" data-level="6.2.2" data-path="writing-functions.html"><a href="writing-functions.html#naming-conventions-1"><i class="fa fa-check"></i><b>6.2.2</b> Naming Conventions</a></li>
<li class="chapter" data-level="6.2.3" data-path="writing-functions.html"><a href="writing-functions.html#function-arguments"><i class="fa fa-check"></i><b>6.2.3</b> Function Arguments</a></li>
<li class="chapter" data-level="6.2.4" data-path="writing-functions.html"><a href="writing-functions.html#function-body"><i class="fa fa-check"></i><b>6.2.4</b> Function Body</a></li>
<li class="chapter" data-level="6.2.5" data-path="writing-functions.html"><a href="writing-functions.html#return-values"><i class="fa fa-check"></i><b>6.2.5</b> Return Values</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="writing-functions.html"><a href="writing-functions.html#documentation-and-commenting"><i class="fa fa-check"></i><b>6.3</b> Documentation and Commenting</a>
<ul>
<li class="chapter" data-level="6.3.1" data-path="writing-functions.html"><a href="writing-functions.html#documenting-functions-with-roxygen2"><i class="fa fa-check"></i><b>6.3.1</b> Documenting Functions with Roxygen2</a></li>
<li class="chapter" data-level="6.3.2" data-path="writing-functions.html"><a href="writing-functions.html#commenting-inside-functions"><i class="fa fa-check"></i><b>6.3.2</b> Commenting Inside Functions</a></li>
</ul></li>
<li class="chapter" data-level="6.4" data-path="writing-functions.html"><a href="writing-functions.html#testing-functions"><i class="fa fa-check"></i><b>6.4</b> Testing Functions</a>
<ul>
<li class="chapter" data-level="6.4.1" data-path="writing-functions.html"><a href="writing-functions.html#why-test-functions"><i class="fa fa-check"></i><b>6.4.1</b> Why Test Functions?</a></li>
<li class="chapter" data-level="6.4.2" data-path="writing-functions.html"><a href="writing-functions.html#writing-simple-tests"><i class="fa fa-check"></i><b>6.4.2</b> Writing Simple Tests</a></li>
<li class="chapter" data-level="6.4.3" data-path="writing-functions.html"><a href="writing-functions.html#automated-testing-with-testthat"><i class="fa fa-check"></i><b>6.4.3</b> Automated Testing with <code>testthat</code></a></li>
</ul></li>
<li class="chapter" data-level="6.5" data-path="writing-functions.html"><a href="writing-functions.html#advanced-function-techniques"><i class="fa fa-check"></i><b>6.5</b> Advanced Function Techniques</a>
<ul>
<li class="chapter" data-level="6.5.1" data-path="writing-functions.html"><a href="writing-functions.html#function-factories"><i class="fa fa-check"></i><b>6.5.1</b> Function Factories</a></li>
<li class="chapter" data-level="6.5.2" data-path="writing-functions.html"><a href="writing-functions.html#closures"><i class="fa fa-check"></i><b>6.5.2</b> Closures</a></li>
<li class="chapter" data-level="6.5.3" data-path="writing-functions.html"><a href="writing-functions.html#vectorised-functions"><i class="fa fa-check"></i><b>6.5.3</b> Vectorised Functions</a></li>
<li class="chapter" data-level="6.5.4" data-path="writing-functions.html"><a href="writing-functions.html#anonymous-functions"><i class="fa fa-check"></i><b>6.5.4</b> Anonymous Functions</a></li>
</ul></li>
<li class="chapter" data-level="6.6" data-path="writing-functions.html"><a href="writing-functions.html#avoiding-common-pitfalls-in-function-writing"><i class="fa fa-check"></i><b>6.6</b> Avoiding Common Pitfalls in Function Writing</a>
<ul>
<li class="chapter" data-level="6.6.1" data-path="writing-functions.html"><a href="writing-functions.html#overloading-functions"><i class="fa fa-check"></i><b>6.6.1</b> Overloading Functions</a></li>
<li class="chapter" data-level="6.6.2" data-path="writing-functions.html"><a href="writing-functions.html#handling-errors-gracefully"><i class="fa fa-check"></i><b>6.6.2</b> Handling Errors Gracefully</a></li>
<li class="chapter" data-level="6.6.3" data-path="writing-functions.html"><a href="writing-functions.html#avoiding-side-effects"><i class="fa fa-check"></i><b>6.6.3</b> Avoiding Side Effects</a></li>
</ul></li>
<li class="chapter" data-level="6.7" data-path="writing-functions.html"><a href="writing-functions.html#summary-4"><i class="fa fa-check"></i><b>6.7</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="error-handling.html"><a href="error-handling.html"><i class="fa fa-check"></i><b>7</b> Error Handling</a>
<ul>
<li class="chapter" data-level="7.1" data-path="error-handling.html"><a href="error-handling.html#introduction-to-error-handling"><i class="fa fa-check"></i><b>7.1</b> Introduction to Error Handling</a>
<ul>
<li class="chapter" data-level="7.1.1" data-path="error-handling.html"><a href="error-handling.html#what-is-error-handling"><i class="fa fa-check"></i><b>7.1.1</b> What is Error Handling?</a></li>
<li class="chapter" data-level="7.1.2" data-path="error-handling.html"><a href="error-handling.html#types-of-errors-in-r"><i class="fa fa-check"></i><b>7.1.2</b> Types of Errors in R</a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="error-handling.html"><a href="error-handling.html#basic-error-handling-with-try-and-trycatch"><i class="fa fa-check"></i><b>7.2</b> Basic Error Handling with <code>try</code> and <code>tryCatch</code></a>
<ul>
<li class="chapter" data-level="7.2.1" data-path="error-handling.html"><a href="error-handling.html#using-try"><i class="fa fa-check"></i><b>7.2.1</b> Using <code>try</code></a></li>
<li class="chapter" data-level="7.2.2" data-path="error-handling.html"><a href="error-handling.html#using-trycatch"><i class="fa fa-check"></i><b>7.2.2</b> Using <code>tryCatch</code></a></li>
<li class="chapter" data-level="7.2.3" data-path="error-handling.html"><a href="error-handling.html#returning-values-from-trycatch"><i class="fa fa-check"></i><b>7.2.3</b> Returning Values from <code>tryCatch</code></a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="error-handling.html"><a href="error-handling.html#custom-error-messages-with-stop-warning-and-message"><i class="fa fa-check"></i><b>7.3</b> Custom Error Messages with <code>stop</code>, <code>warning</code>, and <code>message</code></a>
<ul>
<li class="chapter" data-level="7.3.1" data-path="error-handling.html"><a href="error-handling.html#using-stop-for-critical-errors"><i class="fa fa-check"></i><b>7.3.1</b> Using <code>stop</code> for Critical Errors</a></li>
<li class="chapter" data-level="7.3.2" data-path="error-handling.html"><a href="error-handling.html#using-warning-for-non-critical-issues"><i class="fa fa-check"></i><b>7.3.2</b> Using <code>warning</code> for Non-Critical Issues</a></li>
<li class="chapter" data-level="7.3.3" data-path="error-handling.html"><a href="error-handling.html#using-message-for-informational-messages"><i class="fa fa-check"></i><b>7.3.3</b> Using <code>message</code> for Informational Messages</a></li>
</ul></li>
<li class="chapter" data-level="7.4" data-path="error-handling.html"><a href="error-handling.html#defensive-programming"><i class="fa fa-check"></i><b>7.4</b> Defensive Programming</a>
<ul>
<li class="chapter" data-level="7.4.1" data-path="error-handling.html"><a href="error-handling.html#input-validation"><i class="fa fa-check"></i><b>7.4.1</b> Input Validation</a></li>
<li class="chapter" data-level="7.4.2" data-path="error-handling.html"><a href="error-handling.html#asserting-conditions"><i class="fa fa-check"></i><b>7.4.2</b> Asserting Conditions</a></li>
<li class="chapter" data-level="7.4.3" data-path="error-handling.html"><a href="error-handling.html#handling-edge-cases"><i class="fa fa-check"></i><b>7.4.3</b> Handling Edge Cases</a></li>
</ul></li>
<li class="chapter" data-level="7.5" data-path="error-handling.html"><a href="error-handling.html#best-practices-for-error-handling"><i class="fa fa-check"></i><b>7.5</b> Best Practices for Error Handling</a>
<ul>
<li class="chapter" data-level="7.5.1" data-path="error-handling.html"><a href="error-handling.html#provide-clear-and-informative-messages"><i class="fa fa-check"></i><b>7.5.1</b> Provide Clear and Informative Messages</a></li>
<li class="chapter" data-level="7.5.2" data-path="error-handling.html"><a href="error-handling.html#use-trycatch-for-anticipated-errors"><i class="fa fa-check"></i><b>7.5.2</b> Use <code>tryCatch</code> for Anticipated Errors</a></li>
<li class="chapter" data-level="7.5.3" data-path="error-handling.html"><a href="error-handling.html#log-errors-in-production-code"><i class="fa fa-check"></i><b>7.5.3</b> Log Errors in Production Code</a></li>
<li class="chapter" data-level="7.5.4" data-path="error-handling.html"><a href="error-handling.html#test-error-handling"><i class="fa fa-check"></i><b>7.5.4</b> Test Error Handling</a></li>
</ul></li>
<li class="chapter" data-level="7.6" data-path="error-handling.html"><a href="error-handling.html#summary-5"><i class="fa fa-check"></i><b>7.6</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="version-control-with-git.html"><a href="version-control-with-git.html"><i class="fa fa-check"></i><b>8</b> Version Control with Git</a>
<ul>
<li class="chapter" data-level="8.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#introduction-to-git"><i class="fa fa-check"></i><b>8.1</b> Introduction to Git</a>
<ul>
<li class="chapter" data-level="8.1.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#benefits-of-using-git"><i class="fa fa-check"></i><b>8.1.1</b> Benefits of Using Git</a></li>
</ul></li>
<li class="chapter" data-level="8.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#setting-up-git"><i class="fa fa-check"></i><b>8.2</b> Setting Up Git</a>
<ul>
<li class="chapter" data-level="8.2.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#installing-git"><i class="fa fa-check"></i><b>8.2.1</b> Installing Git</a></li>
<li class="chapter" data-level="8.2.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#configuring-git"><i class="fa fa-check"></i><b>8.2.2</b> Configuring Git</a></li>
</ul></li>
<li class="chapter" data-level="8.3" data-path="version-control-with-git.html"><a href="version-control-with-git.html#basic-git-workflow"><i class="fa fa-check"></i><b>8.3</b> Basic Git Workflow</a>
<ul>
<li class="chapter" data-level="8.3.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#initialising-a-repository"><i class="fa fa-check"></i><b>8.3.1</b> Initialising a Repository</a></li>
<li class="chapter" data-level="8.3.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#staging-and-committing-changes"><i class="fa fa-check"></i><b>8.3.2</b> Staging and Committing Changes</a></li>
<li class="chapter" data-level="8.3.3" data-path="version-control-with-git.html"><a href="version-control-with-git.html#viewing-repository-status"><i class="fa fa-check"></i><b>8.3.3</b> Viewing Repository Status</a></li>
<li class="chapter" data-level="8.3.4" data-path="version-control-with-git.html"><a href="version-control-with-git.html#viewing-commit-history"><i class="fa fa-check"></i><b>8.3.4</b> Viewing Commit History</a></li>
</ul></li>
<li class="chapter" data-level="8.4" data-path="version-control-with-git.html"><a href="version-control-with-git.html#branching-and-merging"><i class="fa fa-check"></i><b>8.4</b> Branching and Merging</a>
<ul>
<li class="chapter" data-level="8.4.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#creating-and-switching-branches"><i class="fa fa-check"></i><b>8.4.1</b> Creating and Switching Branches</a></li>
<li class="chapter" data-level="8.4.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#merging-branches"><i class="fa fa-check"></i><b>8.4.2</b> Merging Branches</a></li>
<li class="chapter" data-level="8.4.3" data-path="version-control-with-git.html"><a href="version-control-with-git.html#resolving-merge-conflicts"><i class="fa fa-check"></i><b>8.4.3</b> Resolving Merge Conflicts</a></li>
</ul></li>
<li class="chapter" data-level="8.5" data-path="version-control-with-git.html"><a href="version-control-with-git.html#working-with-remote-repositories"><i class="fa fa-check"></i><b>8.5</b> Working with Remote Repositories</a>
<ul>
<li class="chapter" data-level="8.5.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#cloning-a-repository"><i class="fa fa-check"></i><b>8.5.1</b> Cloning a Repository</a></li>
<li class="chapter" data-level="8.5.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#before-starting-work-ensure-your-local-repository-is-up-to-date-by-pulling-the-latest-changes"><i class="fa fa-check"></i><b>8.5.2</b> Before starting work, ensure your local repository is up to date by pulling the latest changes:</a></li>
<li class="chapter" data-level="8.5.3" data-path="version-control-with-git.html"><a href="version-control-with-git.html#pushing-changes"><i class="fa fa-check"></i><b>8.5.3</b> Pushing Changes</a></li>
</ul></li>
<li class="chapter" data-level="8.6" data-path="version-control-with-git.html"><a href="version-control-with-git.html#advanced-git-features"><i class="fa fa-check"></i><b>8.6</b> Advanced Git Features</a>
<ul>
<li class="chapter" data-level="8.6.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#stashing-changes"><i class="fa fa-check"></i><b>8.6.1</b> Stashing Changes</a></li>
<li class="chapter" data-level="8.6.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#rebasing"><i class="fa fa-check"></i><b>8.6.2</b> Rebasing</a></li>
<li class="chapter" data-level="8.6.3" data-path="version-control-with-git.html"><a href="version-control-with-git.html#tags"><i class="fa fa-check"></i><b>8.6.3</b> Tags</a></li>
</ul></li>
<li class="chapter" data-level="8.7" data-path="version-control-with-git.html"><a href="version-control-with-git.html#git-in-rstudio"><i class="fa fa-check"></i><b>8.7</b> Git in RStudio</a>
<ul>
<li class="chapter" data-level="8.7.1" data-path="version-control-with-git.html"><a href="version-control-with-git.html#setting-up-git-in-rstudio"><i class="fa fa-check"></i><b>8.7.1</b> Setting Up Git in RStudio</a></li>
<li class="chapter" data-level="8.7.2" data-path="version-control-with-git.html"><a href="version-control-with-git.html#using-git-in-rstudio"><i class="fa fa-check"></i><b>8.7.2</b> Using Git in RStudio</a></li>
</ul></li>
<li class="chapter" data-level="8.8" data-path="version-control-with-git.html"><a href="version-control-with-git.html#best-practices-for-using-git"><i class="fa fa-check"></i><b>8.8</b> Best Practices for Using Git</a></li>
<li class="chapter" data-level="8.9" data-path="version-control-with-git.html"><a href="version-control-with-git.html#summary-6"><i class="fa fa-check"></i><b>8.9</b> Summary</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html"><i class="fa fa-check"></i><b>9</b> Reproducibility and Documentation</a>
<ul>
<li class="chapter" data-level="9.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#introduction-to-reproducibility"><i class="fa fa-check"></i><b>9.1</b> Introduction to Reproducibility</a>
<ul>
<li class="chapter" data-level="9.1.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#what-is-reproducibility"><i class="fa fa-check"></i><b>9.1.1</b> What is Reproducibility?</a></li>
<li class="chapter" data-level="9.1.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#challenges-to-reproducibility"><i class="fa fa-check"></i><b>9.1.2</b> Challenges to Reproducibility</a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#setting-up-a-reproducible-environment"><i class="fa fa-check"></i><b>9.2</b> Setting Up a Reproducible Environment</a>
<ul>
<li class="chapter" data-level="9.2.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#managing-r-and-package-versions"><i class="fa fa-check"></i><b>9.2.1</b> Managing R and Package Versions</a></li>
<li class="chapter" data-level="9.2.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#using-rmarkdown-for-reproducible-reports"><i class="fa fa-check"></i><b>9.2.2</b> Using RMarkdown for Reproducible Reports</a></li>
<li class="chapter" data-level="9.2.3" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#version-control-with-git-1"><i class="fa fa-check"></i><b>9.2.3</b> Version Control with Git</a></li>
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<li class="chapter" data-level="9.3" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#sharing-your-work"><i class="fa fa-check"></i><b>9.3</b> Sharing Your Work</a>
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<li class="chapter" data-level="9.3.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#sharing-code-and-data"><i class="fa fa-check"></i><b>9.3.1</b> Sharing Code and Data</a></li>
<li class="chapter" data-level="9.3.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#creating-reproducible-examples"><i class="fa fa-check"></i><b>9.3.2</b> Creating Reproducible Examples</a></li>
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<li class="chapter" data-level="9.4" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#documentation-for-reproducibility"><i class="fa fa-check"></i><b>9.4</b> Documentation for Reproducibility</a>
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<li class="chapter" data-level="9.4.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#documenting-data"><i class="fa fa-check"></i><b>9.4.1</b> Documenting Data</a></li>
<li class="chapter" data-level="9.4.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#writing-a-readme-file"><i class="fa fa-check"></i><b>9.4.2</b> Writing a README File</a></li>
<li class="chapter" data-level="9.4.3" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#creating-a-reproducibility-checklist"><i class="fa fa-check"></i><b>9.4.3</b> Creating a Reproducibility Checklist</a></li>
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<li class="chapter" data-level="9.5" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#case-study-reproducible-analysis-in-r"><i class="fa fa-check"></i><b>9.5</b> Case Study: Reproducible Analysis in R</a>
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<li class="chapter" data-level="9.5.1" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#overview"><i class="fa fa-check"></i><b>9.5.1</b> Overview</a></li>
<li class="chapter" data-level="9.5.2" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#setting-up-the-project"><i class="fa fa-check"></i><b>9.5.2</b> Setting Up the Project</a></li>
<li class="chapter" data-level="9.5.3" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#documenting-the-analysis"><i class="fa fa-check"></i><b>9.5.3</b> Documenting the Analysis</a></li>
<li class="chapter" data-level="9.5.4" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#sharing-the-project"><i class="fa fa-check"></i><b>9.5.4</b> Sharing the Project</a></li>
<li class="chapter" data-level="9.5.5" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#running-the-analysis"><i class="fa fa-check"></i><b>9.5.5</b> Running the Analysis</a></li>
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<li class="chapter" data-level="9.6" data-path="reproducibility-and-documentation.html"><a href="reproducibility-and-documentation.html#summary-7"><i class="fa fa-check"></i><b>9.6</b> Summary</a></li>
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<li class="chapter" data-level="10" data-path="conclusion.html"><a href="conclusion.html"><i class="fa fa-check"></i><b>10</b> Conclusion</a>
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<li class="chapter" data-level="10.1" data-path="conclusion.html"><a href="conclusion.html#recap-of-key-concepts"><i class="fa fa-check"></i><b>10.1</b> Recap of Key Concepts</a>
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<li class="chapter" data-level="10.1.1" data-path="conclusion.html"><a href="conclusion.html#introduction-1"><i class="fa fa-check"></i><b>10.1.1</b> Introduction</a></li>
<li class="chapter" data-level="10.1.2" data-path="conclusion.html"><a href="conclusion.html#naming-conventions-2"><i class="fa fa-check"></i><b>10.1.2</b> Naming Conventions</a></li>
<li class="chapter" data-level="10.1.3" data-path="conclusion.html"><a href="conclusion.html#organising-scripts-1"><i class="fa fa-check"></i><b>10.1.3</b> Organising Scripts</a></li>
<li class="chapter" data-level="10.1.4" data-path="conclusion.html"><a href="conclusion.html#commenting-code-1"><i class="fa fa-check"></i><b>10.1.4</b> Commenting Code</a></li>
<li class="chapter" data-level="10.1.5" data-path="conclusion.html"><a href="conclusion.html#syntax-and-spacing"><i class="fa fa-check"></i><b>10.1.5</b> Syntax and Spacing</a></li>
<li class="chapter" data-level="10.1.6" data-path="conclusion.html"><a href="conclusion.html#writing-functions-1"><i class="fa fa-check"></i><b>10.1.6</b> Writing Functions</a></li>
<li class="chapter" data-level="10.1.7" data-path="conclusion.html"><a href="conclusion.html#error-handling-1"><i class="fa fa-check"></i><b>10.1.7</b> Error Handling</a></li>
<li class="chapter" data-level="10.1.8" data-path="conclusion.html"><a href="conclusion.html#version-control-with-git-2"><i class="fa fa-check"></i><b>10.1.8</b> Version Control with Git</a></li>
<li class="chapter" data-level="10.1.9" data-path="conclusion.html"><a href="conclusion.html#reproducibility-and-documentation-1"><i class="fa fa-check"></i><b>10.1.9</b> Reproducibility and Documentation</a></li>
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<li class="chapter" data-level="10.2" data-path="conclusion.html"><a href="conclusion.html#the-importance-of-adopting-best-practices"><i class="fa fa-check"></i><b>10.2</b> The Importance of Adopting Best Practices</a></li>
<li class="chapter" data-level="10.3" data-path="conclusion.html"><a href="conclusion.html#moving-forward"><i class="fa fa-check"></i><b>10.3</b> Moving Forward</a></li>
<li class="chapter" data-level="10.4" data-path="conclusion.html"><a href="conclusion.html#final-thoughts-1"><i class="fa fa-check"></i><b>10.4</b> Final Thoughts</a></li>
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