Lab 1 - Data visualization

Lab

Important

This lab is due Thursday, May 25th at 11:59pm ET.

Learning goals

In this lab, you will…

learn how to effectively visualize numeric and categorical data.
continue developing a workflow for reproducible data analysis.

Getting started

Go to the sta199-summer-1 organization on GitHub. Click on the repo with the prefix lab-01. It contains the starter documents you need to complete the lab.
Clone the repo and start a new project in RStudio. See the Lab 0 instructions for details on cloning a repo and starting a new R project.

Packages

We will use the tidyverse package to create and customize plots in R.

library(tidyverse)
library(viridis)

Data: Let’s take a trip to the Midwest

The data in this lab is in the midwest data frame. It is part of the ggplot2 R package, so the midwest data set is automatically loaded when you load the tidyverse package.

The data contains demographic characteristics of counties in the Midwest region of the United States.

Because the data set is part of the ggplot2 package, you can read documentation for the data set, including variable definitions by typing ?midwest in the console.

Exercises

As we’ve discussed in lecture, your plots should include an informative title, axes should be labeled, and careful consideration should be given to aesthetic choices.

In addition, the code should not exceed 80 characters on a given line, so that all the code can be read when you render to PDF. To help with this, you can add a vertical line at 80 characters by clicking “Tools” \(\rightarrow\) “Global Options” \(\rightarrow\) “Code” \(\rightarrow\) “Display”, then set “Margin Column” to 80, and click “Apply”.

Remember that continuing to develop a sound workflow for reproducible data analysis is important as you complete the lab and other assignments in this course. There will be periodic reminders in this assignment to remind you to render, commit, and push your changes to GitHub. You should aim to have at least 3 commits with meaningful commit messages by the end of the assignment.

Make a histogram to visualize the percent college education of counties. Set the binwidth to 2 and include axes labels and a title.
- Describe the shape of the distribution.
- Do there appear to be are any outliers? Briefly explain.

Note

For more details and code examples for histograms ggplot2 reference page.

Create a scatterplot of the percentage of people with a college degree (percollege) versus percentage below poverty (percbelowpoverty) with points colored by state. Label the axes and legend and give the plot a title. Use the scale_color_viridis_d() function to apply the viridis color palette to your plot.

Note

See Introduction to the viridis color maps to read more about the viridis R package and see code examples.

Render, commit, and push your changes to GitHub with the commit message “Added answer for Ex 1 -2”.

Make sure to commit and push all changed files so that your Git pane is empty afterwards.

Describe what you observe in the plot from the previous exercise. In your description, include similarities and differences in the patterns across states.
Now, let’s examine the relationship between the same two variables, using a separate plot for each state. Label the axes and give the plot a title. Use geom_smooth with the argument se = FALSE to add a smooth curve fit to the data. Which plot do you prefer - this plot or the plot in Ex 2? Briefly explain your choice.

Note

se = FALSE removes the confidence bands around the line. These bands show the uncertainty around the smooth curve. We’ll discuss uncertainty around estimates later in the course and bring these bands back then.

Now is another good time to render, commit, and push your changes to GitHub with a meaningful commit message.

Once again, make sure to commit and push all changed files so that your Git pane is empty afterwards.

Do some states have counties that tend to be geographically larger than others? To explore this question, create side-by-side boxplots of area (area) of a county based on state (state).
- Describe what you observe from the plot.
- Which state has the single largest county? How do you know based on the plot?
Do some states have a higher percentage of their counties located in a metropolitan area? Create a segmented (stacked) bar chart with one bar per state and the fill determined by the distribution of metro, whether a county is considered in a metro area. The y-axis of the segmented barplot should range from 0 to 1.
- What do you notice from the plot?

Note

For this exercise, you should begin with the data wrangling code below. We will learn more about data wrangling next week.

midwest <- midwest |>
  mutate(metro = if_else(inmetro == 1, "Yes", "No"))

Now is another good time to render, commit, and push your changes to GitHub with a meaningful commit message.

And once again, make sure to commit and push all changed files so that your Git pane is empty afterwards. We keep repeating this because it’s important. So take a moment to make sure you’re following along with the instructions around Git.

Recreate the plot below.

Hints:

Use theme minimal
The size of the points is 2.
The transparency (alhpa) of the points is 0.5.
You can put line breaks in labels with \n.

Render, commit, and push your final changes to GitHub with a meaningful commit message.

Make sure to commit and push all changed files so that your Git pane is empty afterwards.

Submission

Once you are finished with the lab, you will submit your final PDF document to Gradescope.

Warning

Before you wrap up the assignment, make sure all documents are updated on your GitHub repo. We will be checking these to make sure you have been practicing how to commit and push changes.

You must turn in a PDF file to the Gradescope page by the submission deadline to be considered “on time”.

Make sure your data are tidy! That is, your code should not be running off the pages and spaced properly. See: https://style.tidyverse.org/ggplot2.html.

To submit your assignment:

Go to http://www.gradescope.com and click Log in in the top right corner.
Click School Credentials \(\rightarrow\) Duke NetID and log in using your NetID credentials.
Click on your STA 199 course.
Click on the assignment, and you’ll be prompted to submit it.
Mark all the pages associated with exercise. All the pages of your lab should be associated with at least one question (i.e., should be “checked”).
Do not select any pages of your .pdf submission to be associated with the “Workflow & formatting” question.

Grading (50 pts)

Component	Points
Ex 1	5
Ex 2	6
Ex 3	4
Ex 4	9
Ex 5	6
Ex 6	7
Ex 7	8
Workflow & formatting	5

Note

The “Workflow & formatting” grade is to assess the reproducible workflow. This includes:

linking all pages appropriately on Gradescope
putting your name in the YAML at the top of the document
committing the submitted version of your .qmd to GitHub
Are you under the 80 character code limit? (You shouldn’t have to scroll to see all your code). Pipes %>%, |> and ggplot layers + should be followed by a new line
You should be consistent with stylistic choices, e.g. only use 1 of = vs <- and %>% vs |>
All binary operators should be surrounded by space. For example x + y is appropriate. x+y is not.