Welcome to Infectious Disease Epidemiology - a Model-based Approach. This is a long title, so I’ll be referring to the course as IDEMA for short.
The course is divided into modules. Each module consists of one or several units.
This first module provides a brief introduction to the course, followed by discussing and setting up our various tools and an introduction to the topic.
The specific learning objectives for this module are:
The main goal for this course is for you to learn different concepts of infectious disease (ID) epidemiology from a model-based perspective.
I hope that this course will provide you with a view of infectious diseases at the population level (i.e. infectious disease epidemiology), which complements both a clinical perspective based on individual patients, and a classical epidemiological perspective based on specific study groups and designs (e.g. case-control, cohort and similar studies).
Throughout this course, we will take a systems perspective to understand spread and control of infectious diseases. To give an example: We know that many infectious diseases have temporal patterns. E.g. influenza outbreaks usually occur annually, while measles outbreaks – before widespread vaccination – often occurred in multi-year cycles. What determines such patterns? The classical medical and epidemiological approaches are not well suited to answer this question, but - as we will see in this course - a systems perspective using models as tools for inquiry can answer this and other questions related to population level disease patterns.
The learning objectives listed here are not complete, but cover the significant aspects of the course. By the end of the course, you will be able to:
While the course is all about infectious diseases (ID), we will not spend much time discussing different diseases in detail. Instead, the focus is on overall features and patterns we see among different types of ID. We will of course often use specific ID as examples. In that case, I assume you know some basics of the disease or if you do not, that you will be reading up on it. Knowledge about a specific ID at the level provided by sources such as Wikipedia or CDC is usually enough.
I also assume that you are familiar with public health/epidemiology concepts and terminology at a basic level (incidence, prevalence, different types of study designs, etc.). If you come across concepts or terms that you are unfamiliar with, a quick online search should help fill any gaps.
Since this course takes a model-based approach, you will encounter mathematical and computer models. You will see equations describing specific ID systems, and you will see some R code. However, this course does not cover building and implementing models and how to write code. Instead, you will be interactively exploring already developed computer simulations of infectious disease systems, without the need to write code. You will occasionally have to perform some mathematical manipulations, but those won’t go beyond basic algebra.
I describe my thoughts on teaching and learning a bit more in the completely optional Teaching and Learning thoughts document, which is part of this module. As a summary, here are my goals, promises, and expectations for this course.
I expect you to be self-motivated and committed to learning the material by putting in the effort needed to succeed.
I will try to maximize the rewards you get by hopefully teaching topics you find interesting and useful.
This class strives to be challenging but non-threatening. As such, you will be asked to work hard, and I expect you to do the assigned tasks by the deadlines, but in the end, I usually don’t grade hard - unless you fail to keep up your end of the agreement and don’t put in the work.
This class is open everything. You can use the internet, ask your classmates, myself and others, get help from wherever you can. I trust you will find the right balance of getting help when you need it while still putting in enough effort to experience real learning.
I will not perform any policing to try to prevent you from taking shortcuts (i.e., not doing work yourself). The class contains graded assessments with deadlines; those are meant to help you stay on track. If you cheat - and cheating will be easy - you are mainly cheating yourself out of learning.
Overall, I hope this course is going to be useful, interesting, challenging and also interactive. Online courses are always a bit tricky with interaction/participation. I hope we can create something online that feels like a classroom. Please participate, ask questions, provide feedback, make suggestions for improvements, etc. The more you engage in the course, the more you’ll get out of it.
This is a brief overview of the tools we will be using for this class. They are described in more detail in further documents.
The grade will be made up as follows:
The following grading scale will be used, final grades might be curved (only upward): A 93-100, A- 90-93, B+ 87-90, B 83-87, B- 80-83, C+ 77-80, C 73-77, C- 70-73, D 60-70, F < 60
Most modules have assessments (these are graded). Due dates are usually Friday 5 pm the week of the module. Some might be at other times, e.g., the beginning or middle of the week. You are responsible for keeping up with the due dates. If in doubt, ask.
Every module will have an Assessment document, which describes what work you need to do for that module that will be graded. The following types of assessments are part of the course.
Most course modules have one or more exercises, usually based on the DSAIDE package. Do the exercises at any time, and as you go, fill in the answers to the quiz sheet for that exercise. The Exercises document for each module will provide more details
You will be asked regularly to post discussions to Slack, and respond to posts by others. The general setup, unless otherwise stated, is that you need to post your initial write-up by Wednesday, and post at least 3 replies by the Friday deadline. I also encourage general, continued participation on the discussion boards. Participation can take any form, such as asking questions, answering questions, posting links to interesting content, providing feedback, etc. The more, the better 😄. Both quality and quantity will affect your participation grade. More details are given in either the Exercises or Assessment document for each module.
The project is a semester-long project broken into pieces with several deadlines. The Projects section provides more details.
We’ll be drawing on a lot of different resources. I compiled a list with the ones we’ll use and others you might find helpful in the Resources section of the class website.
Please use the communications tools for this class liberally to ask for help. See the Communication page for more.