Week 12: Applying Your Skills & Moving Forward

Introduction to R Markdown.

R Markdown (`.Rmd`) is a powerful framework that allows you to create dynamic, reproducible documents directly from R. It integrates your R code, the output of that code (including plots and tables), and narrative text (written using Markdown syntax) into a single file.

Why Use R Markdown?

• Reproducibility: Your analysis, results, and explanations are all in one place, making it easy for others (and your future self) to understand and reproduce your work.
• Automation: If your data changes, you simply "knit" the R Markdown document again to update all results and outputs automatically.
• Multiple Output Formats: You can render your `.Rmd` file into various formats like HTML, PDF, Word documents, presentations (slides), dashboards, and more, often with minimal changes to the source file.
• Integration: Seamlessly blends code, output, and text.

Basic Structure

An R Markdown file typically consists of:

1. YAML Header: At the top, enclosed by `---`, specifies metadata like title, author, date, and output format.
2. Markdown Text: Narrative text formatted using standard Markdown syntax (headings, lists, bold, italics, links, etc.).
3. Code Chunks: Blocks of R code enclosed by `` ```{r chunk-name, options} `` and `` ``` ``. When the document is rendered ("knitted"), the code in these chunks is executed, and the results (text output, plots, tables) can be embedded in the final document according to chunk options (e.g., `echo=TRUE` shows code, `eval=TRUE` runs code, `fig.show='hold'` shows plots).

---
title: "My Analysis Report"
author: "Your Name"
date: "`r Sys.Date()`" # R code can be embedded here!
output: html_document
---

## Introduction

This is regular text written using Markdown. We can include **bold** and *italic* text.

Here is an R code chunk:

` `` `{r setup, include=FALSE}
# Chunk options like include=FALSE prevent code and output from appearing
library(tidyverse)
` `` `

## Analysis Section

We loaded the `mpg` dataset earlier. Let's create a plot:

` `` `{r scatterplot, echo=TRUE, fig.cap="MPG Scatter Plot"}
# This code and its output (the plot) will be included
ggplot(mpg, aes(x = displ, y = hwy)) +
  geom_point(aes(color = class)) +
  labs(title = "Displacement vs Highway MPG")
` `` `

The plot above shows the relationship between engine displacement and fuel efficiency.

To create and render R Markdown documents, you'll typically use RStudio, which has excellent built-in support (File > New File > R Markdown..., and the "Knit" button).