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This course is designed to expand on the biostatistical methods covered in Applied Biostatistics II. It introduces generalized linear regression including logistic regression, loglinear models (including Poisson and Negative Binomial models of count data), survival analysis, and longitudinal data including random and mixed effect models.

Materials

Session

Topic

GitHub

Lecture

Lab
1 Multiple linear regression review source HTML PDF watch HTML watch
2 Linear and logistic regression as generalized linear models (GLMs) source HTML PDF watch HTML watch
3 Regression coefficients and model matrices source HTML PDF watch HTML watch
4 Loglinear regression part 1 source HTML PDF watch HTML watch
5 Loglinear models part 2 source HTML PDF watch HTML watch
6 Introduction to censored data, the Kaplan-Meier estimator of survival probability, and the log-rank test. source HTML PDF watch HTML watch
7 Proportional Hazards and AFT models source HTML PDF watch HTML watch
8 Survival analysis part 3 source HTML PDF watch HTML watch
9 Repeated Measures and Longitudinal Data Analysis I source HTML PDF watch HTML watch
10 Repeated Measures and Longitudinal Data Analysis II source HTML PDF watch HTML watch

Cloning course materials (for students)

You can download course materials individually from this website, but it is more convenient to clone all course materials at once. However, cloning requires a system installation of git, and the installation methods depend on your operating system. Here are git installation instructions for RStudio. If you are using RStudio on https://anvil.terra.bio (ask the professor for access with free compute), git is pre-installed so you don’t have to install it. Once you have git working from RStudio, you can do the following to obtain a local copy of all course materials:

  1. In RStudio, select “File - New Project”.
  2. Choose “Version Control” then “Git”.
  3. Enter the URL: https://github.com/waldronbios2/cunybios2.git. Enter any directory name (e.g. “cunybios2”), and click “Browse” to choose the current directory. Then click “Create Project”.

That’s it! You can now find all 10 sessions worth of lecture and lab code in the project files. Open any session folder (e.g. session1/vignettes/session_lecture.Rmd) and click “Knit” to build the lecture slides or lab notes.

Data Science Units

This course is supported by free access to DataCamp for registered students.

Technical notes for teachers

To add a new session to this monorepo:

  1. Create a new directory sessionXX with the session package contents (DESCRIPTION, vignettes/, etc.).
  2. Add the new session to the Suggests and Remotes sections of the top-level DESCRIPTION file.
  3. Update youtubeURLs.csv with links to lecture and lab recordings.
  4. Commit and push:
git add .
git commit -m "add sessionXX materials"
git push origin main