Spring 2021 – Math 150

Methods in Biostatistics

Math 150, Spring 2021

Jo Hardin
2351 Estella Laboratory
jo.hardin@pomona.edu

See Sakai for all relevant links

Office Hours (on Discord, see Sakai for link):

Tuesday 8:30-9:30am PT and 3-4pm PT

Thursday 7-8am PT and 12-2pm PT

Friday 9-10:30am PT

or by appointment

Text: Practicing Statistics, Kuiper & Sklar (CD information (datasets and R code) on Sakai.)

homework assignments

Important Dates:

  • Exam 1 (date: Wednesday, March 17)
  • Exam 2 (date: Wednesday, April 28)
  • Final Data Analysis Project (date: end of semester-ish, likely Thursday May 13, draft assignments will be due earlier)

Handouts:

 

  • Clicker Questions
  • Linear Regression
  • Botox & Cards
  • Case Control (smoking data)
  • Log Reg tests & association (burn data)
  • Interaction & multicolinearity (HERS data)
  • Stepwise logistic regression (HERS data)
  • ROC curves (and R)

Diversity and Inclusion Statement (adapted from Monica Linden, Brown University):

In an ideal world, science would be objective. However, much of science is subjective and is historically built on a small subset of privileged voices. In this class, we will make an effort to recognize how science (and statistics!) has played a role in both understanding diversity as well as in promoting systems of power and privilege. I acknowledge that it is possible that there may be both overt and covert biases in the material due to the lens with which it was written, even though the material is primarily of a scientific nature. Integrating a diverse set of experiences is important for a more comprehensive understanding of science. I would like to discuss issues of diversity in statistics as part of the course from time to time.

Please contact me if you have any suggestions to improve the quality of the course materials.

Furthermore, I would like to create a learning environment for my students that supports a diversity of thoughts, perspectives and experiences, and honors your identities (including race, gender, class, sexuality, religion, ability, etc.) To help accomplish this:

  • If you have a name and/or set of pronouns that differ from those that appear in your official records, please let me know!
  • If you feel like your performance in the class is being impacted by your experiences outside of class, please don’t hesitate to come and talk with me.  You can also relay information to me via your mentors.  I want to be a resource for you. If you prefer to speak with someone outside of the course, the math liaisons, Dean of Students, or QSC staff are all excellent resources.

I (like many people) am still in the process of learning about diverse perspectives and identities. If something was said in class (by anyone) that made you feel uncomfortable, please talk to me about it.  As a participant in course discussions, you should also strive to honor the diversity of your classmates.

Homework:

  • Homework will be assigned from the text, posted online, and due to Gradescope every Friday at midnight PT.
    • One homework grade will be dropped.
    • HW is graded on a scale of 5/4/3/2/1. See the first HW assignment for more information.  One point will be deducted if superfluous information is printed or if assignment is excessively long. 
    • All R HW problems should be turned in as pdf documents compiled from an R Markdown file.  Remember:  knit early and often!
  • For help getting started with Gradescope:
    • Get started page with links: https://www.gradescope.com/get_started
    • First steps: https://www.youtube.com/watch?v=F2e9AK7pNFY
    • Second steps: https://www.youtube.com/watch?v=VMM16gdREfg
    • Annotation and navigation: https://www.youtube.com/watch?v=j–Lu90c_9I
    • How to submit as a student: https://www.youtube.com/watch?v=KMPoby5g_nE

Computing:

  • R and RStudio will be used for all homework assignments.
  • You can use R on the Pomona server: https://rstudio.pomona.edu/ (All Pomona students will be able to log in immediately. Non-Pomona students need to get Pomona login information.)
  • Alternatively, feel free to download R onto your own computer.  R is freely available at http://www.r-project.org/ and is already installed on college computers. Additionally, you are required to install R Studio and turn in all R assignments using R Markdown. http://rstudio.org/.  (You can use the LaTeX compiler at:  https://yihui.name/tinytex/)

Participation:

  • After every single class period, you will turn in the in-class warm-up assignment via Gradescope on Sakai. 
  • Ideally, you will use a scanner app on a mobile device to create .pdf documents of your assignments (any written part of the HW and the warm-ups).  If you do not have access to a scanner app, please let me know ASAP, and we will figure out a way for you to turn in assignments as pdf.
  • This class will be interactive which means that I hope you come to class.  I recognize that not everyone lives in a time zone (or has some other constraint) conducive to being at class.  If you can be in class, I hope you will join us.  If you can’t be in class, you should still stay up with the class materials by watching videos and by turning in daily warm-up assignments.  
  • When you are in breakout rooms working on problems, I hope that you will turn on your camera and interact with your peers!  If you can’t turn on your camera, I hope that you will have a photo of yourself (instead of a black screen) so that our class feels more like a community.
  • This class will be using Discord to stay in touch.  We will have office hours on Discord and it will also serve as a place to ask each other questions and stay up to date with the material.   See Sakai for the Discord login information.

Projects:

  • There will be one research project in the class based primarily on the survival analysis material. You will be able to work in pairs or alone.  More information to come on the project.

Course Goals:

  • to be able to critically evaluate the medical literature with respect to design, analysis, and interpretation of results.
  • to understand the role of inherent variability and keep it in perspective when inferring results to a population.
  • to critically evaluate medical results given in the mainstream media.
  • to read published studies with skepticism. Some people (in all fields!) wrongly believe that all studies published in a peer reviewed publication must be 100% accurate and/or well-designed studies. In this course, you will learn the tools to recognize, interpret, and critique statistical results in the medical literature.

Academic Honesty:

  • We will have take-home asynchronous exams.  As such, you are on your honor to present only your work as part of that assessment.  Below, I’ve provided Pomona’s academic honesty policy.  But before the policy, I’ve given some thoughts on cheating which I have taken from Nick Ball’s CHEM 147 Collective (thank you, Prof Ball!).  Prof Ball gives us all something to think about when we are learning in a classroom as well as on our journey to become scientists and professionals:

There are many known reasons why we may feel the need to “cheat” on problem sets or exams:

      • An academic environment that values grades above learning.
      • Financial aid is critical for remaining in school that places undue pressure on maintaining a high GPA.
      • Navigating school, work, and/or family obligations that  have diverted focus from class.
      • Challenges balancing coursework and mental health.
      • Balancing academic, family, peer, or personal issues.

Being accused of cheating – whether it has occurred or not – can be devastating for students. The college requires me to respond to potential academic dishonesty with a process that is very long and damaging. As your instructor, I care about you and want to offer alternatives to prevent us from having to go through this process. If you find yourself in a situation where “cheating” seems like the only option:

Please come talk to me.  We will figure this out together.

  • Pomona College is an academic community, all of whose members are expected to abide by ethical standards both in their conduct and in their exercise of responsibilities toward other members of the community. The college expects students to understand and adhere to basic standards of honesty and academic integrity. These standards include, but are not limited to, the following:
    • In projects and assignments prepared independently, students never represent the ideas or the language of others as their own.
    • Students do not destroy or alter either the work of other students or the educational resources and materials of the College.
    • Students neither give nor receive assistance in examinations.
    • Students do not take unfair advantage of fellow students by representing work completed for one course as original work for another or by deliberately disregarding course rules and regulations.
    • In laboratory or research projects involving the collection of data, students accurately report data observed and do not alter these data for any reason.

Advice:

  • Please email and / or set up a time to talk if you have any questions about or difficulty with the material, the computing, or the course.  Talk to me as soon as possible if you find yourself struggling. The material will build on itself, so it will be much easier to catch up if the concepts get clarified earlier rather than later.  This semester is going to be fun.  Let’s do it.

Grading:

  • 25% Homework
  • 20% Exam 1
  • 20% Exam 2
  • 25% Survival Analysis Research Project
  • 10% Warm-up exercises