Clinic on Meaningful Modeling of Epidemiological Data

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

  1. Schedule

2021 Schedule

This is an archived version of the schedule from the Schedule clinic.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.

Monday, 28 June

Interactive session 1a

Interactive session 1b

  • 19:30-21:00 Tutorial: Dynamical Fever - computer exercise and discussion (Juliet Pulliam, all faculty assisting)
    • To get started, run the following command at the R Studio command line (after installing the ICI3D package): 
        ICI3D::dynamicalFever()
  • 21:00-21:30 Discussion: Dynamical Fever (John Hargrove)

Individual session 1

Please complete the following between the end of Monday’s interactive session and the beginning of Tuesday’s interactive session.

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Tuesday, 29 June

Interactive session 2a

  • 16:30-17:30 Research Pitches I (Moderator: Jonathan Dushoff)
  • 17:30-17:50 Summary and Discussion: Introduction to thinking about data I (Reshma Kassanjee)
  • 17:50-18:10 Summary and Discussion: Introduction to dynamic modeling of infectious diseases (Zinhle Mthombothi)
  • 18:10–18:30 Parallel sessions
    • Track A - Summary and Discussion: Introduction to infectious disease data (Thumbi Mwangi)
    • Track B - Summary and Discussion: Foundations of dynamic modeling (Cari van Schalkwyk)

Interactive session 2b

  • 19:30-20:00 Tutorial review: Questions about Tutorials 1-3 (Carl Pearson and all)
    • Please be prepared to ask any questions you had from going through Tutorials 1-3.
  • 20:00-21:30 Small group session: research questions for modeling projects (All faculty)

Individual session 2

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Wednesday, 30 June

Interactive session 3a

Interactive session 3b

  • 19:30-19:45 Summary and Discussion: Impact of contact patterns, consequences of heterogeneity, and modeling options (John Hargrove)
  • 19:45-20:30 Computer session: Lab 2 - Consequences of heterogeneity in disease emergence (Carl Pearson and all)
    • To get started, run the following command at the R Studio command line (after installing the ICI3D package): 
        ICI3D::heterogeneityTutorial()
  • 20:30-20:40 Lab 2 Summary (Carl Pearson)
  • 20:40-21:10 Discussion: MMED research projects (Cari van Schalkwyk)
  • 21:10-21:30 Mini-feedback session (Faikah Bruce)

Individual session 3

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Thursday, 1 July

Interactive session 4a

  • 16:30-17:50 Computer session: Model fitting (John Hargrove)
    • 17:50-18:10 (Tutorial wrapup by Jonathan Dushoff) Boxcar Model Slides
    • To get started, run the following command at the R Studio command line (after installing the ICI3D package): 
          ICI3D::hivTutorial()
  • 18:10-18:30 Issues arising (mini-feedback, content in general) (Thumbi Mwangi)

Interactive session 4b

  • 19:30-21:00 Parallel sessions
    • Track A
      • Live lecture: Study Design and Analysis in Epidemiology I: Where does modeling fit? (Cari van Schalkwyk)
      • Computer session: Lab 3 - Study Design in Epidemiology
    • Track B
      • Exercise: Creating a model world to address a research question (Thumbi Mwangi)
  • 21:00-21:30 Discussion: MMED Projects (Zinhle Mthombothi)

Individual session 4

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Friday, 2 July

Interactive session 5a

  • 16:30-16:45 Summary and Discussion: Introduction to statistical philosophy (Reshma Kassanjee)
  • 16:45-17:00 Summary and Discussion: Introduction to Likelihood (Cari van Schalkwyk)
  • 17:00-18:30 Interactive lecture: Participatory coding of a dynamical model (Carl Pearson)

Interactive session 5b

Individual session 5

Reminder:

  • 22:30 Tea with North American Faculty

Saturday, 3 July

(free day)

Sunday, 4 July

(free day)

Monday, 5 July

Reminder:

  • 11:00 Tea with African Faculty

Interactive session 6a

  • 16:30-17:15 Interactive lecture: Data, models and science (Jonathan Dushoff)
  • 17:15-17:30 Organizational session: Schedule and goals for the second week (Rebecca Borchering)
  • 17:30-18:15 Computer session: Introduction to GitHub (discussion and tutorial) (Carl Pearson)
  • 18:15-18:30 Summary and Discussion: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Juliet Pulliam)

Note: Please complete the tutorial review and mentoring sessions questionnaire by 19:30 on Monday!

Interactive session 6b

  • 19:30-20:45 Parallel sessions
  • 20:45-21:30 Work session: Project groups meet for the first time (Work plans for group projects) (all)

Individual session 6

  • Video lecture: Modeling in practice: The life cycle of a modeling project, from conception to publication (John Hargrove)
  • Tutorial catch-up, as needed
  • Work on group project
  • One-on-one mentoring sessions
  • Coding demonstration: Participatory Coding of a Dynamic Model (Steve Bellan) (optional)
    • Note that this is the 2017 version of the participatory coding session that Carl Pearson ran on Friday. The model diagram used in this version comes from the 2017 Creating a Model World session led by Juliet Pulliam, which can be viewed here (also optional).

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Tuesday, 6 July

Interactive session 7a

  • 16:30-17:30 Lecture: Likelihood fitting and dynamic models II (Bobby Reiner)
  • 17:30-18:00 Tutorial review: Q&A on all tutorials to date (Juliet Pulliam and all)
  • 18:00-18:30 Work session: Group projects

Interactive session 7b

Individual session 7

  • Computer Session: Lab 6 - MLE fitting of an SIR model to prevalence data
  • Video lecture: Data wrangling: Data management and cleaning (Thumbi Mwangi)
  • Computer Session: Tutorial 5 - Data cleaning and management in R
  • Video lecture: Real-world example (faculty research presentation): COVID-19 Scenario Modeling Hub Webinar (Rebecca Borchering)
  • Work on group project
  • One-on-one mentoring sessions

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Wednesday, 7 July

Interactive session 8a

Interactive session 8b

Individual session 8

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Thursday, 8 July

Interactive session 9a

  • 16:30-16:45 Summary and Discussion: Model assessment (Jonathan Dushoff)
  • 16:45-16:55 Lab 6 Summary (Bobby Reiner)
  • 16:55-17:10 Summary and Discussion: Faculty research presentation (John Hargrove)
  • 17:10-18:30 Work session: Group projects and One-on-one mentoring sessions (cross-time zone)

Interactive session 9b

  • 19:30-19:50 Labs 7 and 8 Summary (Reshma Kassanjee)
  • 19:50-21:30 Work session: Group projects and One-on-one mentoring sessions

Individual session 9

  • Tutorial catch-up, as needed
  • Work on group project
    • Finalize project presentations and upload to Teams (00_FinalPresentations folder) by 15:30
  • One-on-one mentoring sessions

Reminder:

  • 22:30 Tea with North American Faculty
  • 11:00 Tea with African Faculty

Friday, 9 July

Interactive session 10a

Interactive session 10b