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Foundations of Statistics with R

Darrin Speegle

2018-06-10

Preface
This is a book on probability and statistics suitable for the sophomore or
junior level at university. We assume knowledge of calculus at the level of
Calculus II. We do not assume prior experience with statistics or
programming, though students who have no experience with either
statistics or programming before starting this class should expect to have to
work hard. We will be using R as an integral part of the exposition — you
should not read this book without first getting R Studio installed. We will use
base R for the most part, with the following exceptions:

1. ggplot2 is used for all graphics. We learned ggplot from the

fantastic book, ggplot2 by Hadley Wickham. I strongly encourage
readers to refer to that book whenever they have a question about
plotting.
2. dplyr is used for data manipulation. Whenever a data manipulation
problem gets tricky, we will switch to the methods of dplyr .
3. The gather function from the package tidyr is used in several
places.
4. We will use datasets from ISwR , MASS and Sleuth3 frequently.

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No book like this would be complete without a list of books that would be
useful for the student who wishes to learn more than what is in this book.
Here is a list of other resources that I have enjoyed learning from.

1. ggplot2, by Hadley Wickham, gives a nice overview of the capabilities

of the ggplot2 package. Students interested in data visualization
would find this book interesting.
2. Advanced R, by Hadley Wickham, provides much more information on
R than what we cover in this book. Computer Science students might
enjoy reading this book.
3. The Statistical Sleuth, by Ramsey and Schafer, will help the student
think more like a statistician when dealing with data sets.
4. Modern Applied Statistics with S, by Venables and Ripley, is a more
advanced book.
5. Introductory Statistics with R, by Peter Dalgaard, is a concise
introduction to using R for many types of statistical procedures.
6. Mathematical Statistics with Applications, by Wackerly, Mendenhall and
Schaeffer, is a more mathematical (but still only requiring multivariate
calculus and perhaps basic linear algebra) look at the topics of this
book. Students interested in the theory and proofs behind the material
in this book would enjoy reading it.
7. Datacamp is an on-line, interactive tutorial based method of learning
data science in general, and R in particular.

Our philosophy in this book is to not shy away from messy data sets. We
have relatively extensive sections on getting data into its correct format,
and we have many exercises with dealing with data. I feel that this is an
essential part of the course.

We are assuming a knowledge of calculus through the Fundamental

Theorem of Calculus, some knowledge of infinite series, and integration.
However, the main parts of the book do not require calculus. Proofs of
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some results are provided, but this is not intended to support a proof based
course. I strongly encourage students to understand the proofs, but often
one only wants to understand the proof after understanding the result and
why it is important. When we use mathematical background that some
students may be rusty on, we provide a link to the Wikipedia page on that
topic.

This is book is written in Markdown using the bookdown package. If, or

should I rather say when, you find typos, mistakes or ideas for
improvement, please create a pull request on bitbucket here. The original
idea for a course of this type is due to Michael Lamar. The author thanks
Bryan Clair for his help in writing this book.

This book is made available the Attribution-NonCommercial 4.0

International Creative Commons License. See here for a summary or here
for details. For usage other than that outlined in the license, please contact
Darrin Speegle at Saint Louis University.

0.1 Installing R

Mac Users

1. visit here,
2. Click on the “Download R for (Mac) OS X” link at the top of the page.
3. Click on the file containing the latest version of R under “Files.”
(Currently 3.4.1, as of July 13, 2017).
4. Save the .pkg file, double-click it to open, and follow the installation
instructions.
5. Next we need to install RStudio.
6. Go to www.rstudio.com and click on the “Download RStudio” button.
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7. Click on “Download RStudio Desktop.”

8. Click on the version recommended for your system, or the latest Mac
version, save the .dmg file on your computer, double-click it to open,
and then drag and drop it to your applications folder.
9. Finally we install crucial packages.
10. Open RStudio.
11. At the > prompt inside Console, type (or copy and paste)
install.packages(c("ggplot2", "dplyr", "ISwR", "MASS", "Sleuth3",

"rmarkdown", "tidyr")) .

Windows Users

1. visit here,
2. Click on the “Download R for Windows” link at the top of the page.
3. Click on the “base” link.
4. Click “R-patched.exe” and save the executable file somewhere on your
computer. Run the .exe file and follow the installation instructions.
5. Next we need to install RStudio.
6. Go to www.rstudio.com and click on the “Download RStudio” button.
7. Click on “Download RStudio Desktop.”
8. Click on the version recommended for your system, or the latest
Windows version, and save the executable file. Run the .exe file and
follow the installation instructions.
9. Finally we install crucial packages.
10. Open RStudio.
11. At the > prompt inside Console, type (or copy and paste)
install.packages(c("ggplot2", "dplyr", "ISwR", "MASS", "Sleuth3",
"rmarkdown", "tidyr")) .

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