Data science lifecycle & Exploratory data analysis using visualization

Research Beyond the Lab: Open Science and Research Methods for a Global Engineer

Lars Schöbitz

Feb 29, 2024

Email from GitHub?

While we are getting ready, please check for this email from GitHub and accept the invitation to join the GitHub organisation for the course. Used Gmail to sign up? Check the folders that aren’t your primary inbox (e.g Updates).

Artwork by @allison_horst

Solving coding problems

Tipps for search engines

• Use actionable verbs that describe what you want to do
• Be specific
• Add R to the search query
• Add the name of the R package name to the search query
• Scroll through the top 5 results (don’t just pick the first)

Example: “How to remove a legend from a plot in R ggplot2”

Stack Overflow

What is it?

• The biggest support network for (coding) problems
• Can be intimidating at first
• Up-vote system

Workflow

• First, briefly read the question that was posted
• Then, read the answer marked as “correct”
• Then, read one or two more answers with high votes
• Then, check out the “Linked” posts
• Always give credit for the solution

Tipps for AI tools

• Use actionable verbs that describe what you want to do
• Be specific
• Add R to the search query
• Add the name of the R package name to the search query

Example: “How to remove a legend from a plot in R ggplot2”

Other sources for help

• Posit Community Forum: https://community.rstudio.com/
• Documentation websites: https://ggplot2.tidyverse.org/
• Mastodon tag: #rstats
• Quarto GitHub Discussion: https://github.com/quarto-dev/quarto-cli/discussions

Interaction with GitHub

open GitHub organisation

Bookmark this link in your browser!

github.com/rbtl-fs24

## on GitHub Organisation

• Search for your username in search bar under Repositories

on your repository

on Posit Cloud

Bookmark this link in your browser!

posit.cloud/spaces/484002/content/

on Posit Cloud

Your turn: Introduce yourself to git

1. Open a web browser on your laptop.
2. Navigate to the course website: rbtl-fs24.github.io/website/
3. If you haven’t yet, bookmark the course website
4. In the left-hand menu, click on Module 2, then select am-01: Git configuration
5. Follow the instructions
6. Place a yellow sticky note on your laptop when you have completed the assignment

10:00

Version Control - Terminology

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remember: git commit

remember: git push

remember: git push

collaborate: git clone

track work: git commit

update: git ???

update: git push

git ???

get updates: git pull

Learning Objectives (for this week)

1. Learners can identify four components of a Quarto file (YAML, code chunk, R code, markdown).
2. Learners can list the six elements of the data science lifecycle.
3. Learners can describe the four main aesthetic mappings that can be used to visualise data using the ggplot2 R Package.
4. Learners can control the colour scaling applied to a plot using colour as an aesthetic mapping.
5. Learners can compare three different geoms (bar/col, histogram, point) and their use case.

Data Science Lifecycle

Deep End

via GIPHY

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Add notes

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1. First you must import your data into R. This typically means that you take data stored:

• in a file
• in a database,
• or web application, and load it into R.

2. If you can get your data into R, you can do data science on it!

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1. Once you’ve imported your data, it is a good idea to tidy it.

2. This means to get it into a structure that lets you focus on the questions about your data and not the format it needs to be in

3. This is the step where we spend by far the biggest amount of our time.

4. It has been estimated that we spend about 80% of our time with cleaning and tidying data, so that we can use it fo our analyses.

5. In my courses you will learn how to structure your data in a tidy format as you collect it, and before you import it. A highly underestimated skill.

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1. Once your data is tidy, a common first step is to transform it.

2. This includes

• narrowing in on what interests you (like all people without toilets in one district, or all data from last year)
• creating new variables from existing (like toilet density, as in number of people per toilet)
• calculating summary statistics (like counts or the mean)

Together, tidying and transforming are called wrangling, because getting your data in a form that’s natural to work with often feels like a fight!

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1. Once you have tidy data with the variables you need, there are two main engines of knowledge generation:

• visualization
• and modelling.

2. These have complementary strengths and weaknesses so any real analysis will iterate between them many times.

3. Visualization is a fundamentally human activity. A good visualization will show you things that you did not expect, or raise new questions about the data.

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1. Models are complementary tools to visualization. Once you have made your questions sufficiently precise, you can use a model to answer them.

2. In my courses, they play a very small part, but I am confident that you will be able to enhance your knowledge on modelling once you understand the basic principles of using the R lanuage.

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1. The last step of data science is communication, an absolutely critical part of any data analysis project.

2. It doesn’t matter how well your models and visualization have led you to understand the data, unless you can also communicate your results to others.

3. And this is a part where R has become really strong.

Exploratory Data Analysis with ggplot2

R Package ggplot2

• ggplot2 is tidyverse’s data visualization package
• gg in ggplot2 stands for Grammar of Graphics
• Inspired by the book Grammar of Graphics by Leland Wilkinson
• Documentation: https://ggplot2.tidyverse.org/
• Book: https://ggplot2-book.org

Slide adapted from datasciencebox.org

My turn: Working with R

Sit back and enjoy!

Take a break

Please get up and move! Let your emails rest in peace.

10:00

Code structure

• ggplot() is the main function in ggplot2
• Plots are constructed in layers
• Structure of the code for plots can be summarized as

ggplot(data = [dataset], 
       mapping = aes(x = [x-variable], 
                     y = [y-variable])) +
  geom_xxx() +
  other options

Code structure

ggplot()

Code structure

ggplot(data = gapminder)

Code structure

ggplot(data = gapminder,
       mapping = aes()) 

Code structure

ggplot(data = gapminder,
       mapping = aes(x = continent,
                     y = lifeExp))  

Code structure

ggplot(data = gapminder,
       mapping = aes(x = continent,
                     y = lifeExp)) +
  geom_boxplot() 

Code structure

ggplot(data = gapminder,
       mapping = aes(x = continent,
                     y = lifeExp)) +
  geom_boxplot() +
  theme_minimal()

Polls

Poll 1: What does the thick line inside the box of a boxplot represent?

1. I don’t know
2. the mean of the observations
3. the middle of the box
4. the median of the observations

Poll 2: What percentage of observations are contained inside the box of a boxplot (interquartile range)?

1. I don’t know
2. 25%
3. depends on the median
4. 50%

Poll 3: What is the median of a set of observations?

1. I don’t know
2. The median is the most frequently occurring value in a dataset.
3. The median is the sum of all values in a dataset divided by the number of observations.
4. The median is the point above and below which half (50%) of the observations falls.

Poll 4: If you have the values: 1, 2, 3, and 10: which statistical measure best represents the “true” value?

1. I don’t know
2. The maximum
3. The standard deviation
4. The median

Boxplot, explained

Figure 1: Diagram depicting how a boxplot is created.

• A box that indicates the range of the middle half of the data, a distance known as the interquartile range (IQR), stretching from the 25th percentile of the distribution to the 75th percentile.

• In the middle of the box is a line that displays the median, i.e. 50th percentile, of the distribution.

• These three lines give you a sense of the spread of the distribution and whether or not the distribution is symmetric about the median or skewed to one side.

• Visual points that display observations that fall more than 1.5 times the IQR from either edge of the box. These outlying points are unusual so are plotted individually.

• A line (or whisker) that extends from each end of the box and goes to the farthest non-outlier point in the distribution.

Our turn: md-02-exercises

1. Open posit.cloud in your browser (use your bookmark).
2. Open the rbtl-fs24 workspace for the course.
3. Click Start next to md-02-exercises.
4. In the File Manager in the bottom right window, locate the md-02b-data-visualization.qmd file and click on it to open it in the top left window.

20:00

Take a break

Please get up and move! Let your emails rest in peace.

10:00

Visualizing data

Types of variables

numerical

discrete variables

• non-negative
• whole numbers
• e.g. number of students, roll of a dice

continuous variables

• infinite number of values
• also dates and times
• e.g. length, weight, size

non-numerical

categorical variables

• finite number of values
• distinct groups (e.g. EU countries, continents)
• ordinal if levels have natural ordering (e.g. week days, school grades)

Histogram

• for visualizing distribution of continuous (numerical) variables

ggplot(data = penguins,
       mapping = aes(x = body_mass_g)) +
  geom_histogram()

Barplot

• for visualizing distribution of categorical (non-numerical) variables

ggplot(data = penguins,
       mapping = aes(x = species)) +
  geom_bar()

Scatterplot

• for visualizing relationships between two continuous (numerical) variables

ggplot(data = gapminder_2007,
       mapping = aes(x = gdpPercap,
                     y = lifeExp,
                     size = pop,
                     color = continent)) +
  geom_point() +
  scale_color_colorblind() +
  theme_minimal()

Your turn: md-02-exercises

1. Open posit.cloud in your browser (use your bookmark).
2. Open the rbtl-fs24 workspace for the course.
3. In the File Manager in the bottom right window, locate the md-02c-make-a-plot.qmd file and click on it to open it in the top left window.
4. Follow instructions in the file

15:00

Homework assignments module 2

Module 2 documentation

rbtl-fs24.github.io/website/modules/md-02.html

Homework due date

• Homework assignment due: Wednesday, March 6th
• Correction & feedback phase up to: Tuesday, March 12th

Wrap-up

Thanks! 🌻

Slides created via revealjs and Quarto: https://quarto.org/docs/presentations/revealjs/ Access slides as PDF on GitHub

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