Overview

This course is designed to expand on the biostatistical methods covered
in Applied Biostatistics I. 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	Status	GitHub	Lecture			Lab
1		git clone	HTML	PDF	watch	HTML	watch
2		git clone	HTML	PDF	watch	HTML	watch
3		git clone	HTML	PDF	watch	HTML	watch
4		git clone	HTML	PDF	watch	HTML	watch
5		git clone	HTML	PDF	watch	HTML	watch
6		git clone	HTML	PDF	watch	HTML	watch
7		git clone	HTML	PDF	watch	HTML	watch
8		git clone	HTML	PDF	watch	HTML	watch
9		git clone	HTML	PDF	watch	HTML	watch
10		git clone	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” (no need to save workspace
   image, I never do. That’s a copy of any objects in memory in your R
   session, but you want to create these with your script anyways)
2. Choose “Version Control” then “Git”.
3. Enter the URL: https://github.com/waldronbios2/cunybios2.git .
   Also enter any directory name (e.g. “lectures and labs” or
   “cunybios2”), and click “Browse” to choose the current directory.
   Then click “Create Project”
4. On the bottom left-hand quadrant of RStudio, click “Terminal”. In
   the terminal, enter the following two commands:
   • git submodule init
   • git submodule update

That’s it! You can now find 10 sessions worth of lecture and lab code,
e.g. in “File - Open” or the file browser, click on “Session1” and
“vignettes” to see the lecture and lab materials. Once you open an Rmd
file you can click “Knit” to build it.

Data Science Units

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

Technical notes for teachers

To add a new git submodule to this repo:

First, add the new session to the Suggests and Remotes sections of the
DESCRIPTION file.

Second, invoke the following from within the local waldronbios2 clone
(example for session10):

git submodule add https://github.com/waldronbios2/session10.git`
git commit -am "add session10 submodule"

Finally, update the file youtubeURLs.csv with links to lecture and lab
recordings, then push changes:

git commit -am "add session10 recording links"
git push origin master