Practice 2

PUBH 523/623

Overview

This practice is mostly hands-on. You will set up the real folder structure you will use for the rest of the course, create your R Project, write your first .qmd from scratch, and practice loading packages — all skills you will rely on every week.

Topics covered (Lessons 7–10):

• Folder and file organization
• Quarto and .qmd files
• Packages
• R Projects and working directories

TipNote on ordering

We’re tackling Quarto and .qmd files, even though it comes second in the lesson order. This way you have access to the .qmd as you are working through the rest of the praactice.

Directions

TipHow to use this file

• The boxes with the yellow stripe explain what to do. Keep these in your submitted file.
• Do all your work below and outside of the yellow-striped boxes.
• Please delete the following sections before submitting:
  • Overview
  • Directions
  • Tip boxes (green stripe)
  • Caution boxes / Needed Steps (orange/red stripe)
  • Submission checklist
  • Note on AI usage

Questions

Question 1: Your First Practice .qmd

In Lesson 8, we walked through the three components of a .qmd file: the YAML header, text, and code chunks. In this question, you will demonstrate that you can create, edit, and render a .qmd file correctly.

Part A: Downloading the practice file

WarningTask

Download this practice .qmd from the course GitHub repository, rename it, and save it in your course folder.

1. Download practice_02.qmd from GitHub.
2. Rename the file to Lastname_Firstinitial_Practice_02.qmd (or lastname_firstinitial_practice_02.qmd), replacing with your actual last name and first initial.
3. Save it inside your practice/ folder. You may create a practice_02/ subfolder if you prefer.

TipTip

If you have already done this (you are reading this file in RStudio!), you are all set. Just confirm the file name is correct before moving on.

Part B: Check your YAML header

WarningTask

Scroll to the very top of this file and update the YAML header:

• Replace "Your name here" in author: with your actual name.
• Confirm that date-modified: "today" is present so the date updates automatically each time you render.

Render the document and confirm your name and today’s date appear at the top of the HTML output.

Part C: Add a heading and paragraph

WarningTask

Directly below this callout box, add:

1. A level 3 heading (###) with a title of your choice (something about yourself or why you are taking this course)
2. A short paragraph (2–4 sentences) of text (can be gibberish) under that heading

You can use the Source editor or the Visual Editor.

Add your heading and paragraph here:

Part D: Code chunk options

WarningTask

The code chunk below calculates the mean of a small vector. Adjust the chunk options so that:

• The code is hidden in the rendered output (results still show)
• Warnings are suppressed

x <- c(4, 8, 15, 16, 23, 42)
mean(x)

[1] 18

TipTip

Add the appropriate #| options at the top of the chunk. Refer to the chunk options table in Lesson 8 if you need a reminder.

Part E: Render and confirm

WarningTask

Render this document to HTML and confirm all of the following:

• Your screenshot from Question 1 Part B appears
• Your heading and paragraph from Part C appear
• The code chunk in Part D shows the result but not the code

Question 2: Set Up Your Course Folder

In our lesson on folder and file organization (L7), we learned that every project should live in one well-organized folder. In this question, you will create that folder and use it for the rest of the course.

Part A: Create the folder structure

WarningTask

On your computer, create a folder called PUBH_523_26Su or PUBH_623_26Su somewhere that makes sense (your Documents folder, OneDrive, etc.). Inside it, create the following subfolders (feel free to change some of the subfolders if you have a preferred organization):

PUBH_523_26Su/
├── admin/
├── data_lessons/
├── data_practice/
├── data_project/
│   ├── data_raw/
│   └── data_processed/
├── lessons/
├── practice/
├── project/
└── README.txt

TipTips

• Create README.txt as a plain text file (open Notepad on Windows or TextEdit on Mac, save as .txt).
• Create data_raw/ and data_processed/ inside the data_project/ folder.
• Folder names should be lowercase with underscores — no spaces!
• You can also copy the folders from our shared folder

Part B: Take a screenshot and insert it here

WarningTask

Take a screenshot of your PUBH_523_26Su folder open in your file browser (Finder on Mac, File Explorer on Windows) so that the subfolders are visible and insert in this .qmd.

CautionNeeded Steps

New skill: inserting an image into a .qmd

Quarto makes it easy to embed images using Markdown syntax. Here is how:

Step 1. Save your screenshot somewhere you can find it, ideally in your practice/ folder where you create a practice_02 subfolder. You can name something like practice_02_folders.png.

Step 2. In this .qmd file, insert the image.

• You can do this in the Visual editor by clicking the picture icon () up top and browsing for your file. If you do this, switch to Source editor to see how the picture insert translates to markdown.
• You can do this in the Source editor by typing the following line, replacing the path with your own: ![Caption describing your image](path/to/your/image.png)
  • Note that here() does not work for image paths

Step 3. Render the document and confirm the screenshot appears in the HTML output.

Question 3: Packages

Part A: Load the course packages

WarningTask

In Lesson 9, we learned to use pacman::p_load() to install and load packages in one step. In the code chunk below, use pacman::p_load() to load all of the following packages:

tidyverse, here, readxl, haven, writexl, janitor, rstatix, gt, gtsummary, naniar

# Load all course packages here using pacman::p_load()

TipTip

If pacman itself is not installed yet, run install.packages("pacman") in your Console first (just once, do not put install.packages() in your .qmd!).

Part B: What does each package do?

WarningTask

Fill in the table below. Each package belongs to one of three categories from Lesson 9: loading/saving data, summarizing/visualizing data, or wrangling data. Note one specific thing each package is used for.

Package	Category	One thing it is used for
here
readxl
haven
janitor
gtsummary
dplyr (part of tidyverse)
ggplot2 (part of tidyverse)

TipTip

You can use the ? command in R to learn more about what a package does.

You can also search online for each one! A quick Google search of gtsummary shows me a page on the package

• I see the description: “The {gtsummary} package provides an elegant and flexible way to create publication-ready analytical and summary tables…” which I can put in my table.

Part C: Install vs. load

WarningTask

A classmate wrote the following at the top of their .qmd file. Identify the problem and explain how to fix it.

install.packages("tidyverse")
library(tidyverse)

What is wrong with putting install.packages() inside a .qmd, and what should they do instead?

Write your answer here.

Question 4: Create Your R Project

We learned that an R Project (.Rproj file) sets the working directory automatically so you never need setwd().

Part A: Create the project

WarningTask

Create an R Project inside your existing PUBH_523_26Su folder and open this .qmd from within it.

CautionNeeded Steps

1. In RStudio: File → New Project → Existing Directory
2. Browse to and select your PUBH_523_26Su or PUBH_623_26Su folder
3. Click Create Project
4. Open this .qmd from within the project (use the Files pane or File → Open File)

Your folder should now contain a PUBH_523_26Su.Rproj or PUBH_623_26Su.Rproj file at the top level. From now on, always start your work by clicking this .Rproj file to open RStudio.

TipTip

If you already created your R Project, just make sure you opened this .qmd from within it. You can check the top-right corner of RStudio — it should show your project name, not “Project: (None)”.

Part B: Confirm the working directory

WarningTask

Run the following code in your Console (not in a rendered chunk) and paste the output in the space below.

getwd()

Paste your getwd() output here:

Example: “/Users/yourname/Documents/PUBH_523_26Su”

Part C: Does the working directory match?

WarningTask

Now run getwd() inside a code chunk and render the document. Does the output match what you pasted in Part B? Write 1–2 sentences explaining what you observe.

TipTip

Remove the #| eval: false line from the chunk below so that it runs and displays output when you render.

getwd()

Write your answer here.

Part D: Why not setwd()?

WarningTask

In 1–2 sentences, explain why you should not use setwd() in your .qmd files, and what you should do instead.

Write your answer here.

Question 5: Using here() for file paths

Part A: Explore here()

WarningTask

Run the following code chunk and render the document. Does the output match your getwd() output from Question 4 Part B? Explain in 1 sentence why they match.

TipTip

Remove the #| eval: false line from the chunk below so that it runs and displays output when you render.

pacman::p_load(here)
here()

Write your answer here.

Part B: Build a file path with here()

WarningTask

Imagine you saved a data file called survey_data.csv in your data_practice/ folder. Fill in the here() call below to build the path to that file, then run the chunk to confirm the path looks correct.

Which path style do you prefer and why? (1–2 sentences)

# Remove the ___ and fill in the here() call
file_path <- here("___", "___")
file_path

Write your answer here.

CautionNeeded Steps: two ways to write here() paths

As shown in Lesson 10, you can write the path two ways — both work:

# Option 1: comma-separated (platform-agnostic — preferred)
here("folder", "file")

# Option 2: slash-separated
here("folder/file")

Part C: Console vs. render

WarningTask

Explain in 2–3 sentences: what problem does here() solve that an R Project alone does not fully fix? Think about what happens when you run code in the Console versus when you render a .qmd.

Write your answer here.

Submission Checklist

If having a checklist helps you stay organized, check off each item below as you complete it. You do not need to submit this checklist.

• PUBH_523_26Su (or PUBH_623_26Su) folder created with all subfolders (Q1 Part A)
• Screenshot of folder structure inserted and visible in the rendered HTML (Q1 Part B)
• All course packages loaded successfully with pacman::p_load() (Q2 Part A)
• Package table filled in with category and description for each (Q2 Part B)
• install.packages() question answered (Q2 Part C)
• File downloaded and renamed correctly (Q3 Part A)
• Name updated in YAML header and date appears correctly in rendered HTML (Q3 Part B)
• Level 3 heading and paragraph added (Q3 Part C)
• Code chunk options updated to hide code and suppress warnings (Q3 Part D)
• Document renders with screenshot, heading, and hidden code confirmed (Q3 Part E)
• R Project (.Rproj) created inside your course folder (Q4 Part A)
• getwd() output pasted from Console (Q4 Part B)
• getwd() chunk rendered and output compared to Part B, with explanation (Q4 Part C)
• setwd() question answered (Q4 Part D)
• here() chunk rendered and output match explained (Q5 Part A)
• here() file path filled in and path style preference explained (Q5 Part B)
• Console vs. render question answered (Q5 Part C)
• Document renders to HTML with no errors
• Files named correctly: Lastname_Firstinitial_Practice_02.qmd and Lastname_Firstinitial_Practice_02.html (or lowercase versions)
• Both .qmd and .html submitted to Brightspace

Note on AI usage

I used GenAI (Claude) to help me draft this practice assignment. It helped me brainstorm ideas for the assignment, and I directed it to help you complete the needed tasks that I showed in the lessons.

The submission checklist was Claude’s idea. I really like it! Let me know what you think!