Clinic on Meaningful Modeling of Epidemiological Data

The 13th MMED clinic ~ June 10-29, 2024 ~ Muizenberg, Cape Town, South Africa

  1. Schedule
  2. MMED 2019

Clinic Schedule

This is an archived version of the schedule from the MMED 2019 clinic. Some links may not work at this time.

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.

Sunday, 26 May

  • 12:00 – 17:00 Registration and welcome, AIMS lobby
  • 18:00 – 18:30 Dinner, AIMS Dining Hall

Monday, 27 May

  • 8:00 – 8:25 Registration and welcome, AIMS lobby
    • Please gather in the main lecture hall by 8:30.
  • 8:30 – 9:00 Welcome and Motivation for Workshop (Juliet, Joseph, and John)
  • 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models (Jim)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 10:45 Organizational session: MMED Road Map and programme overview (Juliet)
  • 10:45 – 11:30 Lecture: Introduction to Thinking About Data I (John)
  • 11:30 – 12:30 Lecture: Introduction to dynamic modeling of infectious diseases (Zinhle)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
    • If you plan to use your laptop for the 15:00 computer exercise, Juliet and Cari will help you get set up at 12:30 in the main lecture hall.
  • 14:00 – 15:00 Parallel sessions
    • Track A: Introduction to infectious disease data (Thumbi)
    • Track B: Foundations of dynamic modeling (Jonathan)
  • 15:00 – 15:30 Exercise and discussion: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: Alex)
    • 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 devtools::install_github('ICI3D/ici3d-pkg') in R studio.
    • To run the tutorial (after installing the package), type (ICI3D::dynamicalFever()).
  • 15:30 – 16:00 Tea and poster set-up
    • with Elisha, Laurette, Zinhle
  • 16:00 – 16:50 Exercise and discussion: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: Alex)
  • 16:50 – 17:00 Discussion: Dynamical Fever and Model Worlds (Juliet)
  • 17:00 – 18:00 Poster session I
  • 18:00 – 18:30 Dinner
  • 19:00 – 19:30 Social Activity: Ice breakers (Masimba)
  • 19:30 – 20:30 Social Activity: Card games: Bullsh!t

Tuesday, 28 May

  • 8:30 – 9:15 Lecture: (Hidden) assumptions of simple ODE models (Juliet)
  • 9:15 – 10:00 Live coding session: Introduction to model implementation (Cari)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:15 Parallel sessions
    • Track A: Lecture: Introduction to Thinking About Data II (Jim) - Main lecture hall
    • Track B: Lecture: Basic stochastic simulation models (Becky) - Small lecture hall
  • 11:15 – 12:30 Computer Session: R Tutorials - Lab 1: ODE models in R (Elisha, Laurette, Juliet, Jim, Cari); MedPH break-out group (Becky, Zinhle)
    • 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)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00– 15:30 Parallel sessions
  • 15:30 – 16:00 Tea and poster set-up
    • with Joseph, John, Becky
  • 16:00 – 16:40 Computer Session: R Tutorials continued (Elisha, Laurette, Zinhle, Joseph, Cari)
  • 16:40 – 17:00 Discussion:
  • 17:00 – 18:00 Poster session II
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Computer session (optional): Tutorial catch-up (Jonathan, Jim, Cari)

Wednesday, 29 May

  • 8:30 – 10:15 Lecture: Consequences of heterogeneity, and modeling options (Jonathan) and Computer Session: R Tutorials - Lab 2: Consequences of heterogeneity (Jonathan, Laurette, Zinhle, Joseph, Alex
    • Please use the script on the R Tutorials page and associated data file to complete this tutorial.
    • Lab 2 Summary (Laurette)
  • 10:15 – 10:30 Coffee break
  • 10:30 – 10:45 Sunshine break
  • 10:45 – 11:00 Lecture: Introduction to models and data: HIV in Harare (John)
  • 11:00 – 12:30 Computer Session: Harare data in groups of <4 (Elisha, Jonathan, John, Thumbi, Alex)
    • You will need the ICI3D R package for this tutorial.
    • To run the tutorial (after installing the package), type (ICI3D::hivTutorial()).
    • If you finish all five versions of the model for the Harare data before lunch, move on to working on data from other countries.
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 14:30 Computer Session: Harare/other data in same groups (Becky, John, Laurette, Juliet, Joseph)
  • 14:30 – 15:30 Discussion: Harare tutorial (John)
  • 15:30 – 16:00 Tea and poster set-up
    • with Jonathan, Cari, Alex
  • 16:00 – 17:00 Parallel sessions
    • Track A: Formulating Research Questions A (Zinhle)
    • Track B: Formulating Research Questions B (Becky)
  • 17:00 – 18:00 Poster session III
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Real-world example: Guest lecture (Bobby Reiner)

Thursday, 30 May

  • 8:30 – 10:00 Parallel sessions
    • Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology: Where does modeling fit? (Jim) and R Tutorials - Lab 3: Study Design in Epidemiology (Jonathan, Laurette, Zinhle, Jim, Cari)
    • Lab 3 Summary (Zinhle)
    • Track B: Exercise: Creating a model world to address a research question (Thumbi)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:00 Lecture: Introduction to statistical philosophy (Jonathan)
  • 12:00 – 12:30 Discussion: MMED research projects (Moderator: Becky)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 15:30 Lecture: Participatory coding of a dynamical model (Juliet, with Thumbi) - Code to be added on Tutorials page
  • 15:30 – 16:00 Tea
  • 16:00 – 16:45 Lecture: Introduction to Likelihood (Cari)
  • 16:45 – 18:00 Computer Session: R Tutorials - Lab 5: Introduction to Likelihood Lab (Elisha, Becky, Jonathan, Joseph, Cari)
    • Lab 5 Summary (Cari)
  • 18:00 – 18:30 Dinner
  • 19:30 – 21:00 Social activity: Drumming

Friday, 31 May

  • 8:30 – 10:00 Parallel sessions:
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Juliet)
  • 11:15 - 12:30 Computer Session: Lab 6: MLE fitting of an SIR model to prevalence data (Elisha, Jonathan, Zinhle, Joseph, Cari)
  • 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 17:00 on Friday.)
  • 14:00 – 15:30 Mentor presentations (Mentors); Moderator: John)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:00 MMED Projects (Moderator: Juliet)
    • Sign up for project groups here
  • 17:00 – 18:00 Mid-session Feedback (Moderator: Masimba)
  • 18:00 – 18:30 Dinner
  • 19:30 – 21:30 Social Activity: Movie Night (Perfect Sense)

Saturday, 1 June

  • 9:00 – 10:30 Live coding session: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture (Jonathan)
  • 10:30 – 11:00 A good chance to sign up for project groups and Coffee break
  • 11:00 – 12:30 Computer Session (optional): Tutorial catch-up, as needed (Elisha, Laurette, Juliet, Joseph, Jim)
  • 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
  • 14:00 – Free/working afternoon

Sunday, 2 June

  • Free day – optional group trip to Cape Point
    • We will leave at 10:00. Please meet in the AIMS lobby by 9:55.

Monday, 3 June

  • 8:30 – 9:15 Lecture: Doing Science (Alex)
  • 9:15 – 9:30 Organizational Session: Schedule and goals for the second week (Becky)
  • 9:30 – 10:00 Work Session: Project groups meet for the first time (All instructors)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:30 Computer Session: Introduction to GitHub (Zinhle)
  • 11:30 – 12:30 Work Session: Work plans for group projects (Project groups)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 15:30 Lecture: Likelihood fitting and dynamic models II (Bobby)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
    • 16:30 – 17:30 Mentoring Session: schedule (Alex, John, Juliet, Tendai)
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 GitHub practice and troubleshooting (Juliet) and/or optional tutorial catch-up (Elisha, Zinhle, Thumbi, Alex)

Tuesday, 4 June

  • 8:30 – 10:00 Lecture: Introduction to Monte Carlo Markov Chains (MCMC) (Jonathan) - Slides (180mb read-only powerpoint slide set with embedded movies)
    • Download the lecture locally from an AIMS computer on the desktop if you login as guest or, if you have an AIMS account, find it at /srv/local/guest/Desktop
    • Group photo after this lecture
  • 10:00 – 10:30 Coffee break
  • 10:30 - 11:30 Computer session: MCMC fitting Labs 7-8 in R Tutorials (Becky, Jonathan, Laurette, Joseph, Cari)
  • 11:30 – 12:30 Work Session (Project groups); MedPH break-out group (Becky, Zinhle)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 14:45 Lecture: Data wrangling I: Data management and cleaning (Thumbi)
  • 14:45 – 15:30 Computer session: R Tutorials - Tutorial 5: Introduction to data cleaning (Elisha, Laurette, Zinhle, Thumbi, Juliet)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
    • 16:30 – 17:30 Mentoring Session: schedule - (Jonathan, Juliet, Laurette)
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Real-world example: Guest lecture (Tendai Mugwagwa)

Wednesday, 5 June

  • 8:30 – 9:30 Lecture: Model assessment (Jonathan)
  • 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.)
    • Sign up to go to on Saturday’s field trip by 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 (Becky, Joseph, Juliet, Zinhle)
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Real-world example (optional lecture): Research Talk (Alex)

Thursday, 6 June

  • 8:30 – 9:15 Discussion: Modeling for policy (Tendai)
  • 9:15 - 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.)
  • 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 (Bobby, Elisha, Jonathan, Joseph, Tendai)
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Work session (Project groups)

Friday, 7 June

  • 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 (Cari, Elisha, Thumbi)
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 13:45 – 15:45 Final presentations
  • 15:30 – 16:00 Tea
  • 16:00 – 17:00 Final Feedback Session (Moderator: Masimba)
  • 17:15 – 17:45 Closing session
  • 18:00 – 18:30 Dinner
  • 20:00 – 22:00 Social Activity: Card games

Saturday, 8 June

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