Sixth annual Clinic on Meaningful Modeling of Epidemiological Data
June 1-12, 2015, African Institute for Mathematical Sciences, Muizenberg, Cape Town, RSA
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1. Poster preparation
Prepare a poster presentation to share your research.
- Poster preparation guidelines are available here.
- Be sure to submit your poster by the May 22 deadline, if you would like us to print it for you.
- See this page for poster session assignments.
If you plan to bring a laptop to use during the Clinic, please install the following programs prior to arrival:
- Excel (or a compatible spreadsheet program)
- Git - version control software
- Note that the latest versions of MacOS come with Git installed, so you may not need to install this program.
- SmartGit - a git client and graphical user interface available for Windows, MacOS, and Linux
- Git Bash (Recommended for Windows users only) - command line access to Git on Windows
- R - a statistical programming language (download links for Windows, Linux, and MacOS)
- R Studio - a user interface for R that will be needed for computer exercises (download link)
Please let us know if you have trouble installing any of the above software!
Note: Even if you are not bringing a laptop to the Clinic, you will need access to a computer with both R and R Studio installed to prepare for the Clinic.
3. Introductory tutorials
When you have successfully installed both R and R Studio, please work through these tutorials:
- Tutorial 0: Introduction to R Studio - provides an introduction to the user interface
- Tutorial 1: Introduction to R and its quirks (required)
- Tutorial 2: More on Vectors, Data Frames, and Functions (required)
- Tutorial 3: Probability Distributions and Control Structures (required)
Tip: To download all of the tutorials at once into a single directory on your computer, you can clone the ICI3D R tutorials repository. You can get started quickly by opening the RTutorials.Rproj file within that directory.
4. Recommended Readings
For all participants
- Heesterbeek, JAP, RM Anderson, V Andreasen, S Bansal, D De Angelis, C Dye, KTD Eames, WJ Edmunds, SDW Frost, S Funk, TD Hollingsworth, T House, V Isham, P Klepac, J Lessler, JO Lloyd-Smith, CJE Metcalf, D Mollison, L Pellis, JRC Pulliam, MG Roberts, C Viboud, and the Isaac Newton Institute IDD Collaboration. (2015) Modeling infectious disease dynamics in the complex landscape of global health. Science 347(6227): aaa4339. doi:10.1126/science.aaa4339
We have put together an introductory overview, which includes excerpts from the below papers.
- Bellan, SE, JRC Pulliam, JC Scott, J Dushoff and the MMED Organizing Committee. How to make epidemiological training infectious. PLoS Biology 2012; 10: e1001295.
- Susser, M and E Susser. Choosing a future for epidemiology: I. Eras and paradigms. Am J Public Health 1996; 86: 668–73.
- Koopman, JS and JW Lynch. Individual causal models and population system models in epidemiology. Am J Public Health 1999; 89: 1170–4.
- Brauer, F. Mathematical epidemiology is not an oxymoron. BMC Public Health 2009; 9: S2.
Especially for those new to dynamical modeling
- Welte, A, B Williams, and G Hitchcock. Mathematical models of transmission and control of infectious agents, Chapter 5.18 in Oxford Textbook of Global Public Health (Sixth Edition, Eds. R Detels, M Gulliford, QA Karim, and CC Tan). Oxford University Press (February 2015). Print ISBN-13: 9780199661756