R Markdown for FW 536 — install, knit, and submit

Why R Markdown

R Markdown lets you write a single document that contains:

• Narrative prose explaining what you did and why.
• Live R code that runs and produces output (numbers, plots, tables).
• Math equations rendered nicely.
• Photos of hand-written work for problems best done on paper.

When you "knit" the document, R Markdown runs all the code, captures the output, and produces a polished HTML file you can submit. The grader sees both your reasoning and your code in one place — which is exactly how scientific writing should work.

Install — do this BEFORE Day 1

1. R (the language)

Download from cran.r-project.org. Pick your platform; install the most recent stable release.

2. RStudio (the editor)

Download the free RStudio Desktop from posit.co/download/rstudio-desktop. Install after R.

3. R Markdown and knitr packages

Open RStudio and run, in the Console pane:

install.packages(c("rmarkdown", "knitr"))

RStudio may also prompt you to install these the first time you open a new R Markdown file — accept the prompt.

4. (Optional but recommended) Pandoc

RStudio ships with a bundled Pandoc, so you usually don't need to install it separately. If knitting fails with a "pandoc not found" error, install it from pandoc.org/installing.html.

Your first R Markdown document

1. In RStudio: File → New File → R Markdown…
2. Choose HTML as the output format. Give the document a title (e.g., "FW536 — Day 1 morning lab — YourName").
3. RStudio creates a starter .Rmd with example content.
4. Click the Knit button (a yarn-and-needles icon at the top of the editor).
5. RStudio renders the document and opens it in a viewer pane and as a .html file in your working directory.

If this works, you're ready. The rest of this tutorial covers the parts of R Markdown you'll use most often.

Code chunks

An R Markdown document is text with embedded code "chunks." A chunk looks like:

```{r}
x <- rnorm(100)
mean(x)
hist(x)
```

Everything inside the triple-backtick block is R code; it will be executed when you knit, and the output (numbers, plots) is inserted into the HTML in place.

Chunk options

You can add options inside the curly braces to control how the chunk behaves:

The most useful default for FW 536 assignments: leave echo ON so graders can see your code; turn message and warning OFF for clean output.

Markdown text

Outside of chunks, you use Markdown to format prose. The most useful patterns:

Math

R Markdown HTML supports LaTeX-style math via MathJax (included automatically).

• Inline math: wrap with single dollar signs. $\mu = \beta_0 + \beta_1 x$ → $\mu = \beta_0 + \beta_1 x$.
• Display math (centered, own line): wrap with double dollar signs.

  $$
  P(\theta \mid y) = \frac{P(y \mid \theta) P(\theta)}{P(y)}
  $$

Useful symbols: \alpha, \beta, \theta, \mu, \sigma, \lambda, \sum, \int, \frac{a}{b}, \sqrt{x}, x^2, x_i, \hat{\beta}, \bar{y}, \to, \ge, \le, \sim.

Adding photos of hand-written work

For probability derivations, Punnett squares, or any work that's faster on paper, you can photograph the page (or scan it) and embed the image in R Markdown.

Step 1 — get the photo onto your computer

• Phone camera → AirDrop / Google Drive / email to yourself.
• Or use a phone scanner app (Adobe Scan, CamScanner, Apple Notes) that exports a clean PDF or PNG.
• Crop and rotate if needed.

Step 2 — save the image alongside your .Rmd file

Create a folder named images/ in the same directory as your .Rmd, and drop the photo in there. Suggested naming: problem3_derivation.jpg.

Step 3 — insert the image in R Markdown

Two equally good ways:

Option A — Markdown syntax

![Caption goes here](images/problem3_derivation.jpg)

Option B — knitr code chunk (gives more control)

```{r, echo=FALSE, out.width="60%", fig.cap="Hand-derivation of Problem 3"}
knitr::include_graphics("images/problem3_derivation.jpg")
```

Step 4 — make sure the image fits

If the photo is huge, restrict width with out.width="60%" (a percentage of the page width) or out.width="400px" (fixed pixels).

The YAML header

Every R Markdown file starts with a YAML block between two --- lines. A good default for FW 536:

---
title: "FW 536 — Day 2 afternoon lab — YourName"
author: "Your Name"
date: "`r Sys.Date()`"
output:
  html_document:
    self_contained: true
    toc: true
    toc_depth: 3
    toc_float: true
    code_folding: show
    theme: cosmo
---

• self_contained: true bundles images and CSS into the HTML so you upload one file.
• toc: true generates a clickable table of contents.
• toc_float: true floats the TOC on the side for easy navigation.
• code_folding: show lets the grader collapse code chunks they don't want to read in detail.
• theme: cosmo picks a clean visual theme.

Knitting to HTML

Press the Knit button (or use the keyboard shortcut Ctrl/Cmd-Shift-K). RStudio will:

1. Run every R code chunk in order.
2. Collect outputs (text, numbers, plots).
3. Render the prose, math, and images.
4. Save a .html file in the same folder as your .Rmd.

If a chunk has an error, knitting stops at that chunk. Read the error message, fix the code, and re-knit.

Submitting to Canvas

1. Knit your .Rmd to HTML (with self_contained: true in the YAML).
2. Find the resulting .html file in your working directory.
3. Open the Canvas assignment for the lab.
4. Upload the .html file. (If you also want to upload the .Rmd source, that's welcomed — it helps the grader help you on partial credit.)
5. Submit before the deadline.

Troubleshooting common errors

A working template

Download rmarkdown_tutorial_starter.Rmd for a known-good starter file. Open it in RStudio, knit it once to confirm everything works, then save a copy and re-use it for every FW 536 lab.

Per-lab R Markdown templates are also provided alongside each problem set in the day's folder (e.g., Day1_Probability/morning_lab_template.Rmd). Start from those — they pre-set the right title and chunks so you can focus on the content.