Stat 145
Intro Biostatistics
Fall 2020


[RStudio@Calvin] [Dope Sheets] [From Class] [Calendar] [Test Info] [IMS text] [IMS errata] [Homework]

Instructor

Randall Pruim
office: North Hall 284
E-mail: rpruim@calvin.edu

You can also message me in Teams if you prefer.

Time/Location

Monday, Tuesday, Wednesday, Friday 9:00 - 10:00, primarily online

Office Hours

I’m usually available immediately after class. I’ll schedule and announce other “official office hours” times as well, often coordinated with problem sets are due.

But we can make arrangements for other times as well. Catch me after class, or send me an email or Teams message with some times that work for you.

Internet Resources

Email

I will maintain an email list of all students registered in this class and will occasionally use it to distribute information and reminders of various things pertaining to this course. If you prefer to read your email from an account other than your calvin student account and do not have it set up to forward automatically, send me email with the email address you prefer.

Please check your email daily. You are responsible for any information communicated via email.

Note: I plan to send email to both our course list and to MS Teams, at least to start the term. That way you will have two places you can find it. If that redundancy is annoying, we can revisit this.

MS Teams

MS Teams will be our main platform for interactive remote learning. Remote class sessions will happen here, for example. But Teams can be used for other things as well:

  • Office hours.
  • Chat (for sending messages to me or to other students)
  • Video meetings: You could even set up video meetings to study with other students if meeting in the same space isn’t possible.

Web Pages

In addition to this home page, I will also maintain a list of web resources pertaining to this course. You are responsible for any information appearing on the course web pages. Items I have prepared and maintain online include

  • a calendar to give you an overview of the semester.

  • daily dope sheets which give the details for each day.

  • a list of homework assignments and due dates.

  • information about tests and exams (appearing shortly before each test date).

For quick access to these and other resources, see the navigation bar at the top of this page.

Moodle

I won’t be using Moodle as the primary organiztional structure for this course, but I’ll put a link there to the online materials, and we will use the quiz feature of moodle for some quizzes, homework, and tests.

Gradescope

You should already have received an invitation to Gradescope. Gradescope (https://www.gradescope.com/) is a system for submitting homework. Basically you scan your hand-written work to a PDF or upload PDFs that you create some other way (Word, RStudio, etc.) Gradescope provides a nice grading interface and has the potential to give you better feedback than most other systems I have seen.

Some instructions/tutorials

Gradescope can also handle things like multiple choice and the like, but for those sorts of items, we are more likely to use Moodle, I think.

Other Important Information

See me

If you are having difficulty with any portion of the course, do not hesitate to contact me. Do this as soon as possible, certainly well in advance of any deadlines (like tests) so that we can work to fix the problem.

Textbook

We will be using online resources for this course. These will include

  • Two Open Intro books

    • IMS: Introduction to Modern Statistics (prelimary edition) by Mine Çetinkaya-Rundel and Johanna Hardin

      • This book is being actively developed, so in addition to getting to use a brand new book, we’ll have some opportunities to provide feedback to the authors
    • ISLBS: Introductory Statistics for the Life and Biomedical Sciences by Julie Vu and David Harrington

      • This book is available as a PDF that you ‘purchase’, but you get to set the purchase price, including $0. But feel free to spend a few dollars to support the authors if you like.

      • Once you have “purchased” the book, you can also download “extras”. These include a tablet friendly version with smaller page margins.

    • You will notice a great deal of similarity between these two books because they are part of a joint Open Intro project and I believe both of them are revisions of an earlier Open Intro statistics book.

      • ISLBS has more of a biological flavor
      • IMS is more general and introduces statisticdal inference via simulations (randomization and bootstrap)
  • Additional materials that I provide for specific topics.

Student Learning Objectives

After this course, students will be able to:

  1. Explain how to use an appropriately designed experiment, observational study, or survey to answer biological questions.
  2. Organize, display, and summarize categorical and quantitative data.
  3. Use models, confidence intervals and hypothesis tests to make inferences about a population based on a sample drawn from the population.
  4. Understand how statistics can be used to pursue truth and identify how its misuse can hide the truth.
  5. Critically evaluate journal articles or media pieces that use the statistical methods covered in the course.
  6. Use technology (particularly R and RStudio software), as appropriate, for each of the out- comes listed above.

Since this course meets the mathematics core requirement, it also satis es the following learning objectives (via the more specific learning outcomes listed above). After the course, students will:

  1. Demonstrate understanding of formal mathematical structures and their applications.
  2. Use mathematical reasoning to solve problems and draw conclusions.
  3. Identify ways that mathematics and the mathematical sciences shape human perspectives.

Grading

Grading will be based on the following approximate weighting:

  • Homework, Labs, Quizzes, etc: 15%

    • Don’t let the low percentage here deceive you – doing homework is essential to learning the material in this class. But homework is primarily for learning, and for finding out what you do and do not understand.
  • Tests and Projects: 60%

    • Each test will be cumulative, but it will emphasize the most recent material.
    • Details about what is covered, test format, etc. will be available in advance of each test.
    • Tests should be taken when they are scheduled. I do not generally offer make-up, alternate or late tests. Instead, if you miss one test (for any reason) or if your final exam score is better than your worst test, then your final exam score will be substituted for that test.
  • Final Exam: 25%

    • The final exam will be cumulative.

    • If your final exam is better than your worst test, then I will replace your worst test score with your final exam score.

Technology

When we need a statistics package in this course to ease our calculations or visualizations, we will use a program called R. R is a very powerful statistical tool and programming language and is being actively developed by statisticians from all over the world who contribute to the main program, its interface, or the many add-on modules (called packages) that are available to handle specialized tasks. R is free and available for Mac, PC, or Linux. It has also been installed on the computers in the Mathematics and Statistics Computer Lab (basement of North Hall) and on some other machines around campus (CS lab and Engineering lab, I think).

The RStudio company has provided an excellent integrated development environment for R. This is the current best and easiest way to use R. Furthermore, we have set up an RStudio server on campus that allows you to run R in a web browser without any need to install the software yourself. Your session is restored each time you return, and you can work on multiple computers without losing your work when you move from one to another.

If you prefer to install R and RStudio on your own machine, the software is free and easy to install on Macs, PCs, and linux boxes. You can get R at http://cran.r-project.org/ and and RStudio at http://rstudio.org/download/desktop. You will also need to install a few R packages, most notably:

  • tidyverse
  • mosaic
  • openintro

Let me know if you want to install R and RStudio locally and have any trouble.

Special Circumstances

Occasionally there are special circumstances that require that the class policies be adjusted for a particular student. In such cases, it is the responsibility of the student to inform me of the situation as soon as possible, so that the appropriate arrangements can be made. This includes, but is not limited to, students with documented disabilities.

Calvin University has a continuing commitment to providing reasonable accommodations for students with documented disabilities. Like so many things this fall, the need for accommodations and the process for arranging them may be altered by the COVID-19 changes we are experiencing and the safety protocols currently in place. Students with disabilities who may need some accommodation in order to fully participate in this class are urged to contact Disability Services in the Center for Student Success (disabilityservices@calvin.edu) as soon as possible to explore what arrangements need to be made to assure access. The three of us (student, instructor, and Disability Services) will work together to come up with an appropriate solution.