Reorganized the first half of the textbook -- up to the new chapter 6

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Old structure: Part 1: Getting Started in R Chapter 1: Installing R Chapter 2: RStudio Projects Chapter 3: R Coding Basics Chapter 4: Workflows for R Coding Chapter 5: Using R Markdown Chapter 6: R Tutorial Exercise

New structure: Part 1: Getting Started in R Chapter 1: Intro to R and RStudio (intro.Rmd) Chapter 2: R Studio Projects (r-studio-projects.Rmd) Chapter 3: How to Use This Textbook (this_textbook.Rmd) Part 2: How to Code in R Chapter 4: R Coding Basics (running-r-code.Rmd) Chapter 5: Workflows for R Coding (r-workflows.Rmd) Chapter 6: Using R Markdown (r-markdown.Rmd) Chapter 7: R packages and Tidyverse

Updated up to the new chapter 6 based on our meeting discussion.

Changes overview:

• Renumbered and renamed "section" into "part"
• Chapter 1: Removed package subsection
• Chapter 2: Added a subsection on the sneak peek at R markdown files
• Chapter 3: How to Use This Textbook (newly added)
• Chapter 4 (previous chapter 3): Added the main header “Part 2: How to Code in R” at the beginning, removed anything related to packages, added more examples and explanation on R built-in functions, and corrected the statement that says read.csv() is a tidyverse function.
• Chapter 5: Changed .r to .rmd explanations for the entire chapter.
• Chapter 6: Added an explanation on the differences between R script and R markdown, added improved explanations of creating code chunks and running code in R markdown.

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Aug 20th Update:

Changes overview:

• Chapter 1: Added an exercise section at the end of the material.
• Chapter 2: Added an exercise section at the end of the material.
• Chapter 3: NA
• Chapter 4 (previous chapter 3): Added information on if-else, loops, and defining functions. Added corresponding exercise questions.
• Chapter 5: NA (The newly added chapter 5 exercise file is identical to the previously reviewed chapter 4's exercise file. Sorry for the confusion caused by moving the file into a different folder.)
• Chapter 6: NA
• Chapter 7 (newly added -- R Packages and Tidyverse): Created the chapter material, as well as an exercise file with a sample csv file provided for one of the problems.

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Aug 26th Update:

General Updates:

• Docs Folder: Updated with the most recent HTML files.
• Rmd Files: Reformatted selected Rmd files based on their build results.
• Readme File: Updated with instructions for bookdown.
• Bookdown.yml: Aligned with the revised textbook structure.

Specific Chapter Updates:

Chapter 3:

• Added guidelines on viewing raw Rmd files for curious learners.
• Introduced the search function with a practical example using tidyverse.

Chapter 4:

• Omitted advanced topics and revised exercises to align with this change.

Chapter 6:

• Emphasized table formatting and introduced the tablegenerator website as a resource.
• Introduced LaTeX:
  • Explained its purpose.
  • Demonstrated how to use display and inline expressions.
  • Highlighted basic LaTeX syntax and provided additional resources.
• Incorporated a section discussing knit options.
• Detailed the reasons scientists opt for R markdown, emphasizing report writing and other applications.
• Enhanced content structure through revised headings and subheadings.

Chapter 7:

• Transitioned from highlighting individual tidyverse packages to a function-centric approach.
• Introduced the smile library with a foundational template.

These modifications reflect the feedback from our last meeting.

NOTE: The latest commit I made includes automatic changes in many files from the docs folder. Please ignore anything that comes from this folder, thanks for understanding!