[In these modules, students will become familiar with basic concepts that will enable them to fit the parameters of a mathematical model, such that the model gives a good description of a data set. Sources of data useful to mathematical epidemiology will be discussed, including online sources of data, and how to extract data sources from the literature using programs like DataThief.
Goodness-of-fit statistics will be discussed, as will computational methods for finding model parameters that optimize the goodness-of-fit statistic. In particular, in the examples we will focus on fitting the parameters of compartmental models of disease dynamics to epidemic data.
In passing along the way, we will discuss how to do literature searches, how to build an annotated bibliography in bibtex, how to come up with a solid research question, how to organize your work, and how to write a good research paper (essentially, many of the skills needed to excel at research!)]
Part I
- Good work habits, and requirements for homework
- Difference between mathematical and statistical modeling
- Where to find sources of data: finding free online data
- Literature searches with Google Scholar
- Where to find sources of data: extracting data from graphs in publications
- Basics of LaTeX and BibTeX
- Simple compartmental modelling in R
Part II
- Optimizing model parameters to data (aka “inverse problems”)
- Optimization example: optimizing parameters of an SIR model to influenza data