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.

Monday, 28 June

Interactive session 1a

Interactive session 1b

  • 20:30-22:00 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()
      
  • 22:00-22:30 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:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Tuesday, 29 June

Interactive session 2a

  • 17:30-18:30 Research Pitches I (Moderator: Jonathan Dushoff)
  • 18:30-18:50 Summary and Discussion: Introduction to thinking about data I (Reshma Kassanjee)
  • 18:50-19:10 Summary and Discussion: Introduction to dynamic modeling of infectious diseases (Zinhle Mthombothi)
  • 19:10–19:30 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

  • 20:30-21:00 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.
  • 21:00-22:30 Small group session: research questions for modeling projects (All faculty)

Individual session 2

Reminder:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Wednesday, 30 June

Interactive session 3a

Interactive session 3b

  • 20:30-20:45 Summary and Discussion: Impact of contact patterns, consequences of heterogeneity, and modeling options (John Hargrove)
  • 20:45-21:30 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()
      
  • 21:30-21:40 Lab 2 Summary (Carl Pearson)
  • 21:40-22:10 Discussion: MMED research projects (Cari van Schalkwyk)
  • 22:10-22:30 Mini-feedback session (Faikah Bruce)

Individual session 3

Reminder:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Thursday, 1 July

Interactive session 4a

  • 17:30-18:50 Computer session: Model fitting (John Hargrove)
    • 18:50-19:10 (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()
      
  • 19:10-19:30 Issues arising (mini-feedback, content in general) (Thumbi Mwangi)

Interactive session 4b

  • 20:30-22:00 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)
  • 22:00-22:30 Discussion: MMED Projects (Zinhle Mthombothi)

Individual session 4

Reminder:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Friday, 2 July

Interactive session 5a

  • 17:30-17:45 Summary and Discussion: Introduction to statistical philosophy (Reshma Kassanjee)
  • 17:45-18:00 Summary and Discussion: Introduction to Likelihood (Cari van Schalkwyk)
  • 18:00-19:30 Interactive lecture: Participatory coding of a dynamical model (Carl Pearson)

Interactive session 5b

Individual session 5

Reminder:

  • 23:30 Tea with North American Faculty

Saturday, 3 July

(free day)

Sunday, 4 July

(free day)

Monday, 5 July

Reminder:

  • 12:00 Tea with African Faculty

Interactive session 6a

  • 17:30-18:15 Interactive lecture: Data, models and science (Jonathan Dushoff)
  • 18:15-18:30 Organizational session: Schedule and goals for the second week (Rebecca Borchering)
  • 18:30-19:15 Computer session: Introduction to GitHub (discussion and tutorial) (Carl Pearson)
  • 19:15-19:30 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 20:30 on Monday!

Interactive session 6b

  • 20:30-21:45 Parallel sessions
  • 21:45-22:30 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:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Tuesday, 6 July

Interactive session 7a

  • 17:30-18:30 Lecture: Likelihood fitting and dynamic models II (Bobby Reiner)
  • 18:30-19:00 Tutorial review: Q&A on all tutorials to date (Juliet Pulliam and all)
  • 19:00-19:30 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:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Wednesday, 7 July

Interactive session 8a

Interactive session 8b

Individual session 8

Reminder:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Thursday, 8 July

Interactive session 9a

  • 17:30-17:45 Summary and Discussion: Model assessment (Jonathan Dushoff)
  • 17:45-17:55 Lab 6 Summary (Bobby Reiner)
  • 17:55-18:10 Summary and Discussion: Faculty research presentation (John Hargrove)
  • 18:10-19:30 Work session: Group projects and One-on-one mentoring sessions (cross-time zone)

Interactive session 9b

  • 20:30-20:50 Labs 7 and 8 Summary (Reshma Kassanjee)
  • 20:50-22:30 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 16:30
  • One-on-one mentoring sessions

Reminder:

  • 23:30 Tea with North American Faculty
  • 12:00 Tea with African Faculty

Friday, 9 July

Interactive session 10a

Interactive session 10b