Sixth annual Clinic on Meaningful Modeling of Epidemiological Data

June 1-12, 2015, African Institute for Mathematical Sciences, Muizenberg, Cape Town, RSA

Return to the Main Page.

Return to the Schedule.

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.

2. Software installation

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:

If you are unfamiliar with or rusty on your understanding of the Binomial Distribution, you may also want to work through the introductory Binomial Distribution tutorial.

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.

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