Clinic Schedule
- Catch up session: sign up here.
- The content below is for 2026.
- Links to R tutorials and exercises are available here.
- As they become available, session slides will appear in this shared folder.
- Foundation materials, used by students completing degrees at the African Institute for Mathematical Sciences - South Africa (AIMS-SA) as extra preparation before MMED, can be found here.
- Unless otherwise noted, all materials made available through this website are licensed through a Creative Commons Attribution-Noncommercial license, detailed at https://creativecommons.org/licenses/by-nc/4.0/.
Participants
Week 1
Day 0 (Sunday, 14 June)
- On arrival Organizational 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 - Belinda
- 07h30-08h20 Organizational session: Registration (Faikah, and Mentors, Lobby)
- 07h45-08h15 Breakfast
- 08h30-09h00 Organizational session: Welcome and motivation for workshop (Carl, Main Hall)
- Notes: General
- 09h00-09h15 Organizational session: MMED roadmap and program overview (Carl, Main Hall)
- Notes: General
- 09h15-10h00 Lecture: Public health, epidemiology, and models (Carl, Main Hall)
- Notes: Jonathan, Shadé
- 10h00-10h30 Coffee
- check morning’s recordings - Faikah
- 10h30-11h45 Lecture: Introduction to dynamic modelling of infectious disease I (Jonathan, Main Hall)
- Notes: CarL, Brian
- 11h45-12h30 Lecture: Introduction to infectious disease data (Mutono, Main Hall)
- Notes: CarL, Shadé
- Day 1 AM Quiz Open
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 13h15-13h45 Technical assistance for participants (AIMS tutors, Comp. Lab)
- AIMS tutors: to hand over any queries to mentors
- 14h00-15h30 Lab-based exercise: Dynamical fever (Mutono, Comp. Lab)
- Launch from R prompt with
ICI3D::dynamicalFever()- Mentors: all
- Faculty: Jonathan, CarL
- Launch from R prompt with
- Summary: Dynamical fever (Mutono, Comp. Lab)
- 15h30-16h00 Tea
- 16h00-17h00 R Tutorial: Tutorial 4 - Visualizing infectious disease data (Belinda, Comp. Lab)
- Walkthrough: Visualization
- Mentors: Brian, Shadé
- Faculty: CarL, Mutono
- Slides: Study design
- Lab 3 - Study design I (may also be of interest, but is an own-time activity)
- 17h00-18h00 Posters: Session 1 (Main Hall)
- Prompt presenters to bring along their own notebooks to keep track of their feedback.
- No Day 1 Afternoon Quiz!
- 18h00-18h30 Dinner
- 18h45-20h00 Social event: Ice-breaker (Faikah, Main Hall)
Day 2 (Tuesday, 16 June)
- 07h45-08h15 Breakfast
- 07h30? whatsapp checkin - Belinda
- 08h30-09h30 Lecture: Introduction to dynamic modelling of infectious disease II (Jonathan, Main Hall)
- Notes: CarL, Belinda
- 09h30-10h15 Live coding: Introduction to model implementation in R (Jonathan, Main Hall)
- Resulting code
- Notes: CarL, Belinda
- 10h15-10h45 Coffee
- 10h45-11h30 Lecture: (Hidden) assumptions of simple ODE models (Carl, Main Hall)
- Notes: Jonathan, Belinda
- 11h30-12h15 Lab: ODE models in R (Brian, Comp. Lab)
- Walkthrough: ODE models
- Mentors: Shadé, Belinda
- Faculty: Lauren, CarL
- 12h15-12h30 Catch-up session: (Mentors, Comp. Lab)
- Mentors: Brian, Shadé, Belinda
- Faculty: Lauren
- Day 2 AM Quiz Open
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-14h45 Lecture: Data management and wrangling (Mutono, Comp. Lab)
- Notes: CarL, Lauren
- 14h45-15h30 R Tutorial: Tutorial 5 - Data wrangling (Shadé, Comp. Lab)
- Walkthrough: Data wrangling
- Mentors: Brian, Belinda
- Faculty: CarL
- 15h30-16h00 Tea
- 16h00-17h00 Exercise: Formulating research questions (Lauren, Jonathan, Mutono, and Carl, Section 1, Section 2)
- ICI3D: assisted by Brian, Shadé, Jonathan
- AIMS: assisted by Belinda, CarL - 17h00-17h05 Poster setup: move desks and chairs
- 17h05-18h00 Posters: Session 2 (Main Hall)
- 18h00-18h30 Dinner
- 19h00-20h00 Guest lecture: Geographic and Age-Based Projection of Immunity: Application to Measles in North Carolina (Claire, Main Hall)
- Moderator: (Carl)
Day 3 (Wednesday, 17 June)
- 07h45-08h15 Breakfast
- 07h30? whatsapp checkin
- 08h30-10h00 Lab-based exercise: Introduction to models and data: HIV in Harare (Carl, Comp. Lab)
- Notes: Lauren
- 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: Lauren
- 10h00-10h30 Coffee
- 10h30-12h00 Lecture: Introduction to statistical philosophy (Jonathan, Main Hall)
- Notes: CarL, Brian
- 12h00-12h30 Projects: Introduction to project topics (Lauren, Main Hall)
- Sign-up for projects
- All
- Day 3 AM Quiz Open
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h30 Exercise: Creating a model world to address a research question (Lauren, Jonathan, Mutono, and Carl, Section 1, Section 2)
- Example
- ICI3D: assisted by Brian, Shadé, Jonathan
- AIMS: assisted by Belinda, Reshma, CarL
- 15h30-16h00 Tea
- 16h00-17h00 Lecture: Introduction to likelihood (Jonathan, Main Hall)
- Notes: CarL, Brian
- 17h00-18h00 Lab: Introduction to likelihood (Jonathan, Comp. Lab)
- MME calculation script
- Walkthrough: Likelihood
- Mentors: all
- Faculty: CarL
- 18h00-18h30 Dinner
- 19h00-20h00 Catch-up session: (Mentors, Comp. Lab)
- Participants should show up in the first 10 minutes. If nobody shows up in that time, the session will be cancelled.
- Faculty: Mutono
Day 4 (Thursday, 18 June)
- 07h45-08h15 Breakfast
- 07h30? whatsapp checkin
- 08h30-10h00 Participatory coding: Building a deterministic model (Carl, Main Hall)
- Resulting code
- Notes: Shadé, Belinda, Mutono
- 10h00-10h30 Coffee
- 10h30-11h30 Lecture: An introduction to stochastic models (Reshma, Main Hall)
- Notes: CarL, Shadé
- 11h30-12h30 Lab: An introduction to stochastic models (Lauren, Comp. Lab)
- Walkthrough: Stochastic models
- Mentors: Shadé, Belinda
- Faculty: Mutono
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-14h45 Lecture: Consequences of heterogeneity and modelling options (Jonathan, Main Hall)
- Notes: Lauren, Mutono, Belinda, Brian
- Drum on the drums; remind them about assessment
- 14h45-15h30 Lab: Consequences of heterogeneity (Jonathan, Comp. Lab)
- Download lab and supplementary functions
- Walkthrough: Heterogeneity
- Mentors: Brian, Belinda
- Faculty: CarL, Reshma, Mutono
- Download lab and supplementary functions
- 15h30-16h00 Tea
- 16h00-16h45 Lecture: Fitting dynamical models I (Carl, Main Hall)
- Notes: Belinda, Lauren, Jonathan
- 16h45-18h00 Lab: Maximum likelihood: fitting of a dynamical model (Carl, Comp. Lab)
- Walkthrough: CarL
- Mentors: Brian, Shadé
- Faculty: Jonathan, CarL, Mutono
- Day 4 Quiz Open!
- 18h00-18h30 Dinner
- 18h30-19h00 Catch-up session: (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 Exercise: Describing a model and its assumptions (Lauren, Jonathan, Mutono, and Carl, Section 1, Section 2)
- NB: Fritz Hahne room has been confirmed for the AIMS participants
- ICI3D: assisted by Brian, Shadé, Jonathan
- AIMS: assisted by Belinda, Reshma, CarL
- Telephone!
- 10h00-10h30 Coffee
- 10h30-11h45 Participatory coding: Building a stochastic model (Carl, Main Hall)
- Resulting code
- Notes: Lauren, Belinda
- 11h45-12h30 Projects: Questions for project topics (Lauren, Main Hall)
- All
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h00 Lecture: Fitting dynamical models II (Jonathan, Main Hall)
- Notes: CarL, Belinda, Lauren
- 15h00-15h30 Catch-up session: (Mentors, Comp. Lab)
- Includes selecting project: Project selection form
- Faculty: Lauren, Mutono
- 15h30-16h00 Tea
- 16h00-17h00 Mentor presentations (Chair: Reshma, Main Hall)
- We don’t take formal notes here; you are requested to communicate privately with the mentors
- 17h00-18h00 Course evaluation: Mid-clinic feedback session (Faikah, Main Hall)
- Project group: work on group assignments possibly calling on experts
- Jonathan, Mutono
- 18h00-18h30 Dinner
- 19h00-21h00 Social event: Movie night (Main Hall)
Day 6 (Saturday, 20 June)
- 08h00-09h00 Breakfast
- 07h30? whatsapp checkin
- 09h00-10h00 Projects: 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 Projects: First group meeting - with advisor Group Breakouts
- Group locations
- 11h30-12h00 Projects: 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;
- 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
Week 2
Day 8 (Monday, 22 June)
- 07h45-08h15 Breakfast
- 08h30-08h45 Organizational session: Feedback responses; review schedule and goals (Reshma, Main Hall)
- Notes: Lauren, Shadé
- 08h45-09h30 Lecture: Life cycle of a modeling project (Carl, Main Hall)
- Notes: Lauren, Reshma
- 09h30-10h00 Projects: Recap of expectations (Lauren, Main Hall)
- Notes: Reshma, Brian
- 10h00-10h30 Coffee
- 10h30-11h30 Lecture: Introduction to health economics in dynamic modelling (Mmamapudi, Main Hall)
- Notes: Mutono, Brian, Jonathan, Belinda
- 11h30-12h30 Lab: Introduction to health economics in dynamic modelling (Mmamapudi, Comp. Lab)
- Walkthrough: Health Economics Model
- Mentors: All
- Faculty: Mutono, Lauren
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h30 Projects: MMED project work (Group Breakouts)
- 15h30-16h00 Tea
- 16h00-18h00 Projects: MMED project work + mentoring sessions (Group Breakouts)
- Faikah will post the session on the door
- Link to mentoring session: here
- 18h00-18h30 Dinner
Day 9 (Tuesday, 23 June)
- 07h45-08h15 Breakfast
- 08h30-10h00 Lecture: Introduction to Markov Chain Monte Carlo (MCMC) (Carl, Comp. Lab)
- Lab: Understanding MCMC (Carl, Comp. Lab)
- Lab: MCMC model fitting (Carl, Comp. Lab)
- Walkthrough: CarL
- Mentors: All
- Faculty: Mutono, Claire Eva
- 10h00-10h30 Coffee
- 10h30-11h30 Lab: above continued (Carl, Comp. Lab)
- Summary: MCMC (Carl, Comp. Lab)
- 11h30-12h30 Lecture: Revision session (Jonathan, Main Hall)
- Notes:
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h30 Projects: MMED project work (Group Breakouts)
- Link for keeping track of projects - Final outputs
- 15h30-16h00 Tea
- 16h00-18h00 Projects: MMED project work + mentoring sessions (Group Breakouts)
- 16h00-16h45 - Switch up day
- Link to mentoring session: here
- Faikah will post the session on the door
- 18h00-18h30 Dinner
- 18h30-19h30 Catch-up session: (Mentors, Comp. Lab)
- Sign up form
- Faculty: CarL, Claire, Lauren
Day 10 (Wednesday, 24 June)
- 07h45-08h15 Breakfast
- 08h30-09h00 Lecture: Study design, bias, variability (Jonathan, Main Hall)
- Notes: Reshma, Belinda, Reshma, Lauren
- 09h00-10h00 Participatory coding: Study design and simulation-based validation (Jonathan, Main Hall)
- 10h00-10h30 Coffee
- Group photo - in front of AIMS door * Shared Google photos folder (only for 2026)
- 10h30-12h30 Projects: MMED project work (Group Breakouts)
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h30 Projects: MMED project work (Group Breakouts)
- 15h30-16h00 Tea
- 16h00-18h00 Projects: MMED project work + mentoring sessions (Group Breakouts)
- Link to mentoring session: here
- 18h00-18h30 Dinner
- 19h00-20h00 Guest lecture: Navigating Shared Modelling, (Vincent, Main Hall)
- Moderator: Jonathan
Day 11 (Thursday, 25 June)
- 07h45-08h15 Breakfast
- 08h30-10h00 Projects: MMED project work (Group Breakouts)
- 10h00-10h30 Coffee
- 10h30-12h30 Projects: MMED project work + mentoring sessions (Group Breakouts)
- Link to mentoring session: here
- 12h30-14h00 Lunch
- 13h00-13h30 faculty meeting - 103
- 14h00-15h30 Options:
- 15h30-16h00 Tea
- 16h00-17h30 Panel discussion: Modelling for policy (Eva, Main Hall)
- Belinda, Brian - mics for Q&A
- Reminder: participants won’t have support for the group work after dinner!
- 18h00-18h30 Dinner
- 19h00-20h00 Projects: MMED project work (Group Breakouts)
- Mentor dinner (full team)
- meet in front of Empire from 17h50
Day 12 (Friday, 26 June)
- 07h45-08h15 Breakfast
- 08h30-08h40 Organizational session: Closing - AIMS Director (Main Hall)
- 08h40-12h30 Projects: MMED project work (Group Breakouts)
- 10h00-10h30 Coffee
- 12h30 Report and presentation due - upload here
- 12h30-13h30 Lunch
- 13h00-13h30 faculty meeting - 103
- 13h30-15h30 Projects: Project presentations (Lauren, Main Hall)
- Remember assessment!
- Report rubric
- Presentation rubric
- 15h30-16h00 Tea
- 16h00-17h00 Course evaluation: Feedback session II (Faikah, Main Hall)
- Faculty Meeting; Pipeline, etc.
- 17h05-17h20 Organizational session: Closing remarks (Reshma, Main Hall)
- 18h00-18h30 Dinner