Clinic on Meaningful Modeling of Epidemiological Data

The thirteenth MMED clinic ~ June 17-29, 2024 ~ Muizenberg, Cape Town, South Africa

  1. Schedule
  2. MMED 2023

Clinic Schedule

The MMED program includes a number of parallel sessions for participants with different backgrounds. Track A is designed for those with a mathematical background, particularly those who have extensive training and/or experience with differential equation models of infectious disease dynamics. Track B is designed for those with a background in epidemiology and/or statistics, particularly those who are involved in data collection for infectious disease systems.

Day 0 (Sunday 16 June)

  • 14:00 – 18:00 Registration and welcome, AIMS lobby
  • 17:15 – 17:45 Dinner, AIMS Dining Hall NOTE normal time 18:00-18:30; changed due to loadshedding
  • Faculty meeting and dinner in E313 at 18:00.
    • Save food for late-arriving faculty (RB, JD)!

Day 1

Day 2

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 9:15 Lecture: (Hidden) assumptions of simple ODE models (borchering)
    • Note takers: pulliam, reiner
  • 9:15 – 10:00 Live coding session: Introduction to model implementation (vanschalkwyk)
    • Note takers: dushoff, mwangi
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:20 Computer Session: R Tutorials - Lab 1: ODE models in R (brown, sereo, vanschalkwyk, mwangi, nyamai, and pearson); MedPH break-out group (mthombothi)
    • All R tutorials and labs are linked from this page
    • You should have completed R Tutorials I-III prior to the Clinic. If you have not previously used R, we suggest you review these tutorials during this session, as the material they cover form the foundation for the computer sessions throughout the workshop. Please use this opportunity to ask any questions you may have regarding the material in these tutorials.
    • When you have completed Lab 1 (required), you may take a break or move on to Tutorial 4: Visualizing Infectious Disease Data in R (recommended)
  • 12:20 – 12:30 Discussion: Lab 1 Summary (brown)
  • 12:30 – 13:45 Lunch break (Lunch is served from 12:30 to 13:00.)
    • 13:15 Faculty check-in in Room 105
  • 13:45 – 14:45 Parallel sessions NOTE (Note: for this session only, Track A participants may attend the Track B session.)
  • 14:45 – 15:30 Lecture: Consequences of heterogeneity, and modeling options (dushoff) (handouts version)
    • Note takers: reiner, abbott
    • Note for future years: This lecture needs more time!! (see faculty notes doc)
  • 15:30 – 16:00 Tea and poster set-up
    • with mthombothi and mentors
    • Table moving: Becky, Zinhle, Lauren, Bobby, Tumelo, Faikah
  • 16:00 - 17:00 Computer Session: R Tutorials - Lab 2: Consequences of heterogeneity (dushoff, kassanjee, mthombothi, pearson, reiner, and vanschalkwyk)
    • You will need the most recent version of the ICI3D R package for this tutorial. If you are using your laptop for the tutorials, please update the package before you begin by running the command remotes::install_github('ICI3D/ici3d-pkg') in R studio.
    • To run the tutorial (after installing the package), type ICI3D::heterogeneityTutorial().
    • Lab 2 Summary (pearson)
  • 17:00 – 18:00 Poster session II
  • 18:00 – 18:30 Dinner
  • 18:30 – 19:00 Poster set-up
  • 19:00 – 20:00 Poster session III
  • 20:05 Faculty Meeting in E313

Day 3

Day 4

Day 5

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 10:00 Lecture: Introduction to statistical philosophy (dushoff) (handouts version)
    • Note takers: abbott, pearson
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:00 Discussion: MMED research projects (reiner)
  • 11:00 – 12:30 Lecture: Participatory coding of a dynamical model I (pulliam, and mwangi) HIDE - Code on Tutorials page
    • Note takers: dushoff or kassanjee, pearson
    • Code from the session
    • Request that everyone download lab during lunch and charge laptops
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
    • Please fill in this form to indicate what you will work on during the tutorial catch-up session on Saturday and whom you would like to meet for a mentoring session next week. (Due by 19:30 on Friday.)
    • 13:30 Faculty check-in in Room 105
  • 14:00 - 15:00 Mentor presentations (brown, and omondi, Moderator: pearson) NOTE stretch break recommended mid-way
  • 15:00 – 15:45 Lecture: Introduction to Likelihood (vanschalkwyk)
    • Note takers: reiner, borchering
  • 15:45 – 16:15 Tea
    • Faculty/mentor trip to Bluebird Garage - meet in the lobby at 16:00
  • 16:15 – 18:00 Computer Session: R Tutorials - Lab 5: Introduction to Likelihood Lab (brown, kombe, mwangi, omondi, pearson, and vanschalkwyk)
  • 18:00 – 18:30 Dinner
  • 18:30 Faculty Meeting in the Library
  • 19:30 – 21:00 Social activity: Drumming

Day 6

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 9:15 Lecture in the Main Lecture Hall: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (reiner)
    • Note takers: dushoff, borchering
  • 9:15 - 10:30 Computer Session in the Main Computer Lab: Lab 6: MLE fitting of an SIR model to prevalence data (brown, dushoff, kassanjee, kombe, nyamai, reiner, and pulliam)
  • 10:30 – 11:00 Coffee break
  • 11:00 – 12:30 Lecture: Participatory coding of a dynamical model II (pearson, and pulliam) Code on Tutorials page
    • Note takers: mthombothi, dushoff
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 15:00 MMED Projects: Participants ask questions about specific projects (Moderator: borchering, and reiner)
    • Project group sign-up will be available after this session
    • Note takers: nyamai, pulliam
  • 15:00 – 16:00 Mid-session Feedback (Moderator: bruce)
  • 16:00 – 16:30 A good chance to sign up for project groups and Tea
  • 16:30 – 17:30 Computer Session: Tutorial catch-up, as needed (brown, omondi, and sereo)
  • 17:30 – 18:00 A good chance to sign up for project groups
  • 18:00 – 18:30 Dinner
  • 19:00 Party in E313

Day 7

  • 10:00 Deadline to sign up for project groups
  • Free day – optional group trip to Cape Point
    • We will leave at 10:00. Please meet in the AIMS lobby by 9:55. Wear comfortable clothes. We will be going on a boat!
  • Faculty meeting in E313 at 17:30.

Day 8

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 9:15 Lecture: The Lifecycle of a Modelling Project (reiner)
    • Note takers: pearson, pulliam
  • 9:15 – 9:45 Organizational Session: Response to feedback (mwangi)
    • Note takers: borchering
  • 9:45 – 10:00 Organizational Session: Goals and Schedule for Week II (pearson)
    • Note takers: dushoff
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:30 Computer Session: Introduction to GitHub (mthombothi, with pearson, pulliam, abbott, sereo, and vanschalkwyk)
    • Note takers: pearson
  • 11:30 – 12:30 Work Session: Work plans for group projects (Project groups / all instructors) NOTE Project groups meet for the first time
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
    • 13:30 Faculty check-in in Room 105
  • 14:00 – 15:30 Lecture: Likelihood fitting and dynamic models II (reiner)
    • abbott, borchering
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
    • 16:30 – 17:30 Mentoring Session: schedule NOTE In future, don’t do mentoring sessions on first day of projects
  • 17:30-18:20 Faculty Meeting in Room 105
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 GitHub practice and troubleshooting and/or optional tutorial catch-up (brown, mthombothi, omondi, sereo, and pulliam)

Day 9

Day 10

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 9:30 Lecture: Model assessment (Dushoff)
    • Note takers: abbott, pulliam
  • 9:30 - 10:00 Work Session (Project groups)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:30 Work Session (Project groups)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
    • 13:30 Faculty check-in in Room 105
  • 14:00 – 15:30 Work Session (Project groups)
    • 14:00 – 15:30 Optional Session - Live coding: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture (dushoff, and mwangi) NOTE Code on Tutorials page
    • Note takers: vanschalkwyk, borchering
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
    • 16:30 – 17:30 Mentoring Session: schedule
  • 17:30-18:20 Faculty Meeting in Room 105
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Real-world example (optional guest lecture): Health Economics talks from Kaja Abbas and Lander Willem

Day 11

  • 8:00 Faculty check-in in Room 105
  • 8:30 – 10:00 Discussion: Modeling for policy (Panel: Rebecca Borchering, Leigh Johnson, Thumbi Mwangi, Corey Peak, Moderator: pulliam)
    • Note takers: pearson, nyamai, mthombothi
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:30 Work Session (Project groups) - Mentors and Facutly Observers
    • 11:15 – 13:00 Annual faculty meeting in Small Seminar Room
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 15:30 Work Session (Project groups)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
    • 16:30 – 17:30 Mentoring Session: schedule
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Work session (Project groups)
    • 19:00 – whenever Mentor dinner (Olympia Cafe)

Day 12

  • 8:30 – 10:00 Work Session (Project groups)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:30 Work Session (Project groups)
    • 10:30 – 11:30 Mentoring Session: schedule
    • Submit slides by 12:30.
  • 12:30 – 13:45 Lunch break (Lunch is served from 12:30 to 13:00.)
    • 13:15 Faculty check-in in Room 105
  • 13:45 – 15:30 Final presentations (Moderator: pulliam)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:00 Final Feedback Session (Moderator: bruce)
  • 17:15 – 17:45 Closing session (pearson)
  • 18:00 – 18:30 Dinner
  • 20:00 – 22:00 Social Activity: TBD

Day 13

  • Clinic officially ends on Friday, but there will be an optional group trip on Saturday.