Day 0 (Sunday, 14 June)

• On arrival Organizing Session: mentors and tutors will assist with direction to accommodations
• Faculty meeting and dinner in E313 from 16h30; be sure to save food for late arrivals once known

Day 1 (Monday, 15 June)

• 07h30? whatsapp checkin
• 07h30-08h20 Organizing Session: Registration (Faikah, and Mentors, Lobby)
• 07h45-08h15 Breakfast
• 08h30-09h00 Welcome and motivation for workshop (Reshma, Main Hall)
  • Notes: ??
• 09h00-09h45 Lecture: Public health, epidemiology, and models (Carl, Main Hall)
  • Notes: ??
• 09h45-10h00 Organizing Session: MMED roadmap and program overview (Reshma, Main Hall)
• 10h00-10h30 Coffee
• 10h30-11h45 Lecture: Introduction to dynamic modelling of infectious disease I (Reshma, Main Hall)
  • Notes: ??
• 11h45-12h30 Lecture: Introduction to infectious disease data (Eva, Main Hall)
  • Notes: ??
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 13h15-13h45 Technical assistance for participants (Mentors, Comp. Lab)
  • Mentors: all
• 14h00-15h30 Comp. Session: Dynamical fever exercise (Mutono, Comp. Lab)
  • Launch from R prompt with ICI3D::dynamicalFever
    • Mentors: all
    • Faculty: Jonathan, Carii
  • Summary: Dynamical fever (Mutono, Comp. Lab)
• 15h30-16h00 Tea
  • Poster setup: Group 1) (Faikah, and Mentors, Main Hall)
• 16h00-17h00 Comp. Session: R Tutorials: Tutorial 4 - Visualizing infectious disease data (Eva, and Belinda, Comp. Lab)
  • Walkthrough: Belinda
  • Mentors: Brian, Shadé
  • Faculty: CarL, Mutono
  • Slides: Study design
  • Summary: Visualization (Belinda, Comp. Lab)
  • Lab 3 - Study design I (may also be of interest, but is an own-time activity)
• 17h00-18h00 Poster session 1 (Main Hall)
• Possible feedback printout forms/Google form QR to give feedback?
• End of Day Questions
• 18h00-18h30 Dinner
• 18h45-20h00 Ice-breaker (Faikah, Main Hall)

Day 2 (Tuesday, 16 June)

• 07h45-08h15 Breakfast
• 07h30? whatsapp checkin
• 08h30-09h30 Lecture: Introduction to dynamic modelling of infectious disease II (Jonathan, Main Hall)
  • Notes: ??
• 09h30-10h15 Live Coding: Introduction to model implementation in R (Reshma, Main Hall)
  • Resulting code
  • Notes: ??
• 10h15-10h45 Coffee
• 10h45-11h30 Lecture: (Hidden) assumptions of simple ODE models (Cari, Main Hall)
  • Notes: ??
• 11h30-12h15 Comp. Session: R Tutorials: Lab 1 - ODE models (Cari, and Brian, Comp. Lab)
  • Walkthrough: Brian
  • Mentors: Shadé, Belinda
  • Faculty: Lauren, Reshma
  • Summary: ODE models (Brian, Comp. Lab)
• 12h15-12h30 Catch-up (Cari, Comp. Lab)
  • Mentors: Brian, Shadé, Belinda
  • Faculty: Lauren, Reshma
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-14h45 Lecture: Data management and wrangling (Mutono, Comp. Lab)
  • Notes: ??
• 14h45-15h30 Comp. Session: R Tutorials: Tutorial 5 - Data wrangling (Mutono, and Shadé, Comp. Lab)
  • Walkthrough: Shadé
  • Mentors: Brian, Belinda
  • Faculty: CarL, Eva
  • Summary: Data wrangling (Shadé, Comp. Lab)
• 15h30-16h00 Tea
  • Poster setup: Group 2 (Faikah, and Mentors, Main Hall)
  • Don’t move the chairs! Only put the posters up.
• 16h00-17h00 Discussion: Formulating research questions (Cari, Eva, Lauren, and Mutono, Section 1, Section 2)
• ICI3D: assisted by Brian, Shadé, Jonathan
• AIMS: assisted by Belinda, Reshma, CarL - 17h00-17h05 Poster setup: move desks and chairs
• 17h05-18h00 Poster session 2 (Main Hall)
• End of Day Questions
• 18h00-18h30 Dinner
• 19h00-20h00 Lecture: Guest lecture: Title, (Claire, Main Hall)
  • Moderator:

Day 3 (Wednesday, 17 June)

• 07h45-08h15 Breakfast
• 07h30? whatsapp checkin
• 08h30-10h00 Comp. Session: Introduction to models and data: HIV in Harare (Reshma, and Carl, Comp. Lab)
  • Notes: ??
  • Launch from R prompt with ICI3D::hivTutorial
  • If you finish all five versions of the model for the Harare data, move on to working on data from other countries.
  • Additional info: Distributed delay models of survival (Boxcar Models) and example script
  • Summary: Harare tutorial (Carl)
  • Mentors: all
  • Faculty: Eva
• 10h00-10h30 Coffee
• 10h30-12h00 Lecture: Introduction to statistical philosophy (Jonathan, Main Hall)
  • Notes: ??
• 12h00-12h30 Projects: Introduction to project topics (Lauren, Main Hall)
  • All
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Discussion: Creating a model world to address a research question (Cari, Eva, Lauren, and Mutono, Section 1, Section 2)
  • ICI3D: assisted by Brian, Shadé, Jonathan
  • AIMS: assisted by Belinda, Reshma, CarL
• 15h30-16h00 Tea
• 16h00-17h00 Lecture: Introduction to likelihood (Cari, Main Hall)
  • Notes: ??
• 17h00-18h00 Comp. Session: Lab 5 - Introduction to likelihood (Cari, and Mentors, Comp. Lab)
  • Mentors: all
  • Faculty: Jonathan, CarL
  • Summary: Likelihood (Cari, Comp. Lab)
• [End of Day Questions]
• 18h00-18h30 Dinner
• 19h00-20h00 Catch-up Session: Tutorials (Mentors, Comp. Lab)
  • This catch-up is open, but please sign up for future catch-ups
  • Faculty: Eva, Mutono

Day 4 (Thursday, 18 June)

• 07h45-08h15 Breakfast
• 07h30? whatsapp checkin
• 08h30-10h00 Live Coding: Participatory coding: Building a deterministic model (Carl, Main Hall)
  • Resulting code
  • Previous year’s code is generally available here
  • Notes: ??
• 10h00-10h30 Coffee
• 10h30-11h30 Lecture: An introduction to stochastic models (Reshma, Main Hall)
  • Notes: ??
• 11h30-12h30 Comp. Session: An introduction to stochastic models (Lauren, and Reshma, Comp. Lab)
  • Walkthrough: Lauren
  • Mentors: Shadé, Belinda
  • Faculty: Eva, Mutono
  • Summary: Stochastic models (Lauren, Comp. Lab)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-14h45 Lecture: Consequences of heterogeneity and modelling options (Jonathan, Main Hall)
  • Notes: ??
  • Drum on the drums; remind them about assessment
• 14h45-15h30 Comp. Session: Lab 2 - Consequences of heterogeneity (Jonathan, Comp. Lab)
  • Download lab and supplementary functions
  • Walkthrough: Jonathan
  • Mentors: Brian, Belinda
  • Faculty: CarL, Eva, Mutono
  • Summary: Heterogeneity (Jonathan, Comp. Lab)
• 15h30-16h00 Tea
• 16h00-16h45 Lecture: Fitting dynamical models I (Cari, Main Hall)
  • Notes: ??
• 16h45-18h00 Comp. Session: Maximum likelihood: fitting of a dynamical model (Cari, Comp. Lab)
  • Walkthrough: Cari
  • Mentors: Brian, Shadé
  • Faculty: Jonathan, CarL, Eva
  • Summary: Maximum likelihood (Cari, Comp. Lab)
• End of Day Questions
• 18h00-18h30 Dinner
• 18h30-19h00 Catch-up Session: Tutorials (Mentors, Comp. Lab)
  • Includes thinking of project questions
  • Complete model diagram
  • Faculty: Reshma, Lauren
• 19h00-21h00 Social Event: Drumming (Main Hall)

Day 5 (Friday, 19 June)

• 07h45-08h15 Breakfast
• 07h30? whatsapp checkin
• 08h30-10h00 Discussion: Describing a model and its assumptions (Cari, Eva, Lauren, and Mutono, Section 1, Section 2)
  • ICI3D: assisted by Brian, Shadé, Jonathan
  • AIMS: assisted by Belinda, Reshma, CarL
  • Telephone!
• 10h00-10h30 Coffee
• 10h30-12h00 Live Coding: Participatory coding: Building a stochastic model (Carl, Main Hall)
  • Resulting code
  • Notes: ??
• 12h30-12h30 Projects: Questions for project topics (Lauren, Main Hall)
  • All
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h00 Lecture: Fitting dynamical models II (Jonathan, Main Hall)
  • Notes: ??
• 15h00-15h30 Catch-up Session: Tutorials (Mentors, Comp. Lab)
  • Includes selecting project: Project selection form
  • Faculty: Carii, Mutono
• 15h30-16h00 Tea
• 16h00-17h00 Mentor presentations (Reshma, Main Hall)
  • We don’t take formal notes here; you are requested to communicate privately with the mentors
• 17h00-18h00 Mid-clinic feeback session (Faikah, Main Hall)
• End of Day Questions
• 18h00-18h30 Dinner
• 19h00-21h00 Social Event: Movie night (Main Hall)
  • Project group: work on group assignments possibly calling on experts

Day 6 (Saturday, 20 June)

• 08h00-09h00 Breakfast
• 07h30? whatsapp checkin
• 09h00-10h00 Comp. Session: Introduction to GitHub (Lauren, Comp. Lab)
  • Faculty: Jonathan, Vince, CarL
• 10h00-10h30 Projects: Group assignments and expectations (all, Main Hall)
  • Slides (includes milestones)
• 10h30-11h00 Coffee
• 11h00-11h30 Group Work: First group meeting - with advisor Group Breakouts
  • Group locations
• 11h30-12h00 Comp. Session: GitHub practice and questions (Lauren, Comp. Lab)
  • Faculty: Jonathan, Vince, CarL
• 12h00-12h30 Catch up session: (Mentors, Comp. Lab)
  • Faculty: Lauren, Mutono
• 12h45 Social Event: Optional: Group lunch at Kalky’s (costs covered)
  • Reminder - no alcohol can be paid for by us
  • 16h30 post-Kalky’s all hands faculty meeting in E313; beverages provided
• 18h00-18h30 Dinner
  • remainder of meeting in E313

Day 7 (Sunday, 21 June)

• 08h00-09h00 Breakfast
• 09h00 Social Event: Outing: Cape Point National Park; depart 09h00 sharp
• 18h00-18h30 Dinner

Day 8 (Monday, 22 June)

• 07h45-08h15 Breakfast
• 08h30-08h45 Discussion: Feedback responses; Review schedule and goals (Reshma, Main Hall)
  • Notes: ??
• 08h45-09h30 Lecture: Life cycle of a modeling project (Carl, Main Hall)
  • note takers: Mutono, Joe
• 09h30-10h00 Projects: Recap of expectations (Lauren, Main Hall)
• 10h00-10h30 Coffee
• 10h30-11h30 Lecture: Introduction to health economics in dynamic modelling (Mmamapudi, Main Hall)
• 11h30-12h30 Comp. Session: Introduction to health economics in dynamic modelling (Mmamapudi, and Mentors, Comp. Lab)
  • Walkthrough: Mmamapudi
  • Mentors: All
  • Faculty: Carii, (Jonathan and CarL if needed and no other suitable)
  • Summary: Health economics (Mmamapudi, Comp. Lab)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 15h30-16h00 Tea
• 16h00-18h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• End of Day Questions
• 18h00-18h30 Dinner

Day 9 (Tuesday, 23 June)

• 07h45-08h15 Breakfast
• 08h30-10h00 Lecture: Introduction to Markov Chain Monte Carlo (MCMC) (Carl, Comp. Lab)
  • Comp. Session: Lab 7 - Understanding MCMC (Carl, and Mentors, Comp. Lab)
  • Comp. Session: Lab 8 - MCMC model fitting (Carl, and Mentors, Comp. Lab)
  • Notes: ??
  • Walkthrough: CarL
  • Mentors: All
  • Faculty: Carii, Claire, Eva, Jonathan
• 10h00-10h30 Coffee
  • Group photo - in fornt of AIMS door
  • See MMED photo folder (request access if necessary)
• 10h30-11h30 Comp. Session: Lab 7 and Lab 8 continued (Carl, and Mentors, Comp. Lab)
• 11h30-12h30 Lecture: Model assessment (Jonathan, Main Hall)
  • Summary: MCMC (Carl, Comp. Lab)
  • Notes: ??
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Group Work: MMED project work (Group Breakouts)
• 15h30-16h00 Tea
• 16h00-18h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• End of Day Questions
• 18h00-18h30 Dinner
• 12h00-12h30 Catch-up Session: (Mentors, Comp. Lab)
  • Faculty: CarL, Claire, Lauren

Day 10 (Wednesday, 24 June)

• 07h45-08h15 Breakfast
• 08h30-09h00 Lecture: Study design, bias, variability (Jonathan, Main Hall)
• 09h00-10h00 Live Coding: Study design and simulation-based validation (Jonathan, Main Hall)
  • Resulting code
  • Notes: ??
• 10h00-10h30 Coffee
• 10h30-12h30 Group Work: MMED project work (Group Breakouts)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Group Work: MMED project work (Group Breakouts)
• 15h30-16h00 Tea
• 16h00-18h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• End of Day Questions
• 18h00-18h30 Dinner
• 19h00-20h00 Lecture: Guest lecture: Title, (Vincent, Main Hall)
  • Moderator:

Day 11 (Thursday, 25 June)

• 07h45-08h15 Breakfast
• 08h30-10h00 Group Work: MMED project work (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-12h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 either Group Work: MMED project work (Group Breakouts)
• 14h00-15h30 or Live Coding: Building a modelling project pipeline with AI (Carl, Main Hall)
  • Resulting code
  • Notes: ??
• 15h30-16h00 Tea
• 16h00-17h30 Discussion: Modelling for policy (Cari, Main Hall)
  • Notes: ??
  • Reminder: participants won’t have support for the group work after dinner!
• 18h00-18h30 Dinner
• 19h00-20h00 Group Work: MMED project work (Group Breakouts)
• Mentor dinner (full team)

Day 12 (Friday, 26 June)

• 07h45-08h15 Breakfast
• 08h30-12h30 Group Work: MMED project work (Group Breakouts)
• 10h00-10h30 Coffee
  • 12h30 Report due
  • 13h00 Presentations due
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 13h30-15h30 Group Work: Project presentations (Lauren, Main Hall)
  • Notes: ??
• 15h30-16h00 Tea
• 16h00-17h00 Discussion: Feedback session II (Faikah, Main Hall)
• 17h15-17h45 Closing remarks (Reshma, Main Hall)
  • Notes: ??
• 18h00-18h30 Dinner