Some info about this book and term
In the summer of 2020, the world was on fire – COVID was raging, we – especially in Minnesota – were processing the murder of George Floyd and the subsequent uprising etc, the future was unclear. At that point teaching was likely to be entirely online, and I decided to write a digital book for my course (see the 1st edition and 2nd edition). I didn’t really know what I was doing or what my vision was (and to some extent I still do not). There were hiccups: some strangeness in rendering etc, typos, last minute updates, writing at 2am etc etc, but on the whole there were numerous advantages compared to a traditional textbook. I lay these out here:
I think all of these benefits were great, and helped a lot, so I am doing it again. I am updating the previous versions for Fall 2024 –this time as a website.
I know you’re dealing with a lot. Every year students are dealing with a lot – from jobs, to supporting family, to the everyday of being in college and living life etc…. Yet, we are all trying to make the most of life in this era. We want to teach, learn, and grow.
What is more, I believe this content is more important now than it has ever been, statistics is obsessed with the critical evaluation of claims in the face of data, and is therefore particularly useful in uncertain times. Given this focus, and given that you all have different energies, motivations and backgrounds, I am restructuring this course slightly from previous years. The biggest change is a continued de-emphasis on math and programming – that doesn’t mean I’m eliminating these features, but rather that I am streamlining the required math and programming to what I believe are the essentials. For those who want more mathematical and/or computational details (either because you want to push yourself or you need this to make sense of things), I am including a bunch of optional content and support. I am also wrestling with the impact of LLMs in our education (more below).
The content is very important to me. I also care deeply about you. I want to make sure you get all you can / all you need from this course, while recognizing the many challenges we are all facing. One tangible thing I leave you with is this book, which I hope you find useful as you go on in your life. Another thing I leave you with is my concern for your well-being and understanding – please contact me with any suggestions about the pace / content / you of this course and/or any life updates which may change how and when you can complete the work.
My motivating goal for this course is to empower you to produce, present, and critically evaluate statistical evidence — especially as applied to biological topics. You should know that stats models are only models and that models are imperfect abstractions of reality. You should be able to think about how a biological question could be formulated as a statistical question, present graphs which show how data speak to this question, be aware of any shortcomings of that model, and how statistical analysis of a data set can be brought back into our biological discussion.
Students will recognize that data are comprised of observations that partially reflect chance sampling, & that a major goal of statistics is to incorporate this idea of chance into our interpretation of observations. Thinking this way can be challenging because it is a fundamentally new way to think about the world. Once this is mastered, much of the material follows naturally. Until then, it’s more confusing.
That chance influences observations is CRITICAL to statistics (see above). Quantitatively translating these probabilities into distributions and associated statistical tests allows for mastery of the topic.
Not only are results influenced by chance, but factors outside of our focus can also drive results. Identifying subtle biases and non-independence is key to conducting and interpreting statistics.
Recognize how bias can influence our results. What is the difference between Bayesian and frequentist thinking? How can data be visualized effectively? What is the difference between statistical and real-world significance? How do we responsibly present/ interpret statistical results? We will grapple with & answer these questions over the term.
Students will gain an intuitive feel for the meaning of stats words like variance, standard error, p-value, t-statistic, and F-statistic, and will be able to read and interpret graphs, and how to translate linear models into sentences.
Students will be able to utilize the statistical language, R, to summarize, analyze, and combine data to make appropriate visualizations and to conduct appropriate statistical tests.
R, RStudio, and the tidyverseWe will be using R in this course, in the RStudio environment. My goal is to have you empowered to make figures, run analyses, and be well positioned for future work in R, with as much fun and as little pain as possible. RStudio is an environment and the tidyverse is a set of R packages that makes R’s powers more accessible without the need to learn a bunch of computer programming.
Some of you might have experience with R and some may not. Some of this experience might be in tidyverse or not. There will be ups and downs — the frustration of not understanding and/or it not working and the joy of small successes. Remember to be patient, forgiving and kind to yourself, your peers, and me. Ask for help from the internet, your friends, Husain, and Yaniv.
We will using R version 4.0.0 or above, and tidyverse version 1.3.0 or above.
You can download these onto your computer (Make sure the R is version 4.0.0).
install.packages("tidyverse") and then library(tidyverse) to ensure this worked.Alternatively you can simply join the course via RStudioCloud. This could be desirable if you do not want to or have trouble doing this.
This ‘book’ functions as an extensive syllabus and course notes. I will embed youtube videos, app-based demonstrations and class exercises. As noted above, there are some things I will include that will not be necessary for everyone, and I will clearly mark these sections.
I hope that this book provides clear and useful background for the course, and I advise you to regularly go through each book ‘chapter’ for the relevant week. Be sure you get familiar with the content BEFORE class.
Note that this ‘book’ is not the entirety of the course content, and is not an original piece of my own effort – in addition from lifting from a few other course online (with attribution), I also make heavy use of these texts:
The Analysis of Biological Data Third Edition (Whitlock and Schluter 2020): This is the official book of this course, and is a standard biostats textbook, with many useful resources available online. The writing is great, as are the examples. Most of my material originates here (although I occasionally do things a bit differently). This book is officially optional, but students consistently tell me that it is extremely helpful. So, I highly recommend buying it. You can get the newest edition here, but any edition will be pretty useful.
Calling Bullshit (Bergstrom and West 2020): This book is not technical, but points to the big picture concerns of statisticians. It is very practical and well written. I will occasionally assign readings from this book, and/or point you to videos on their website. All readings will be made available for you, but you might want to buy a physical copy.
Fundamentals of Data Visualization (Wilke 2019): This book is free online, and is very helpful for thinking about graphing data. In my view, graphing is among the most important skills in statistical reasoning, so I reference it regularly.
R for Data Science (Grolemund and Wickham 2018): This book is free online, and is very helpful for doing the sorts of things we do in R regularly. This is a great resource.
I will introduce other resources as we go.
I aim to have a majority of the course content available before the term begins. As such you can plan around your likely conflicts.
I am still wrapping my head around the use of large language models in this course and how it shapes what students need to know about data, statistics, and coding. Please bear with me…
Please fill out this pre-class survey
Figure 1: The accompanying preclass survey link.