Clinic Schedule
- The schedule below is mostly final
- Links to R tutorials and exercises are available here.
- As they become available, session slides will appear in this shared folder.
- Unless otherwise noted, all materials made available through this website are licensed through a CC-BY International License.
Participants
Week 0: MMED Foundations
Day 1 (Monday, 9 June)
- 07h45-08h15 Breakfast
- 09h00-09h20 Organizing Session: Introductions, Overview (everyone, Main Hall)
- 09h20-10h30 Discussion: Public health, epidemiology, and infectious disease modelling (Carl, Main Hall)
- Faculty meeting and dinner in E313 from 16h30; be sure to save food for late arrivals once known
- 10h30-11h00 Coffee
- 11h00-12h00 Lecture: Introduction to infectious disease dynamics, Part I (Zinhle, Main Hall)
- 12h00-13h00 Lecture: Simple Models (Carl, Main Hall)
- 13h00-14h00 Lunch
- 14h00-15h30 Comp. Session: Tutorial 1: Introduction to R and Epidemic curves (Tutors, Comp. Lab)
- 15h30-16h00 Free - take a walk!
- 16h00-17h00 Comp. Session: Tutorial 1 cont. (Tutors, Comp. Lab)
- 17h00-17h45 Discussion: How to read a scientific paper (Carl, Main Hall)
- 17h45-18h00 Organizing Session: Introduction to projects (Carl, Main Hall)
- End of Day Questions
Day 2
- 07h45-08h15 Breakfast
- 08h30-09h00 Reading time for a scientific paper
- 09h00-10h30 Lecture: Introduction to infectious disease dynamics, Part II (Zinhle, Main Hall)
- “The” R0 paper (might need unpaywall or similar tools to access)
- 10h30-11h00 Coffee
- 11h00-12h00 Lecture: Dynamics of directly transmitted pathogens (Carl, Main Hall)
- 12h00-13h00 Comp. Session: Tutorial 2: More on Vectors, Data Frames, and Functions, and SEIR (Tutors, Comp. Lab)
- 13h00-14h00 Lunch
- 14h00-15h30 Comp. Session: Tutorial 2 & benchmark questions, and SEIR & Benchmark questions (Tutors, Comp. Lab)
- 15h30-16h00 Free - take a walk!
- 16h00-18h00 Group Work: Project development (Group Breakouts)
- End of Day Questions
Day 3
- 07h45-08h15 Breakfast
- 08h30-09h30 Group Work: Project development (Group Breakouts)
- from 08h30, each group will check in with Carl (odd, in 105) or Zinhle (even, lobby): 08h30 1 and 2, 08h50 3 and 4, 09h10 5 and 6
- Project Groups
- 09h30-10h30 Discussion: How did you read a scientific paper? (Carl, Comp. Lab)
- 10h30-11h00 Coffee
- 11h00-11h45 Lecture: Study Design and Analysis in Epidemiology: Where does modeling fit? (Carl, Main Hall)
- 11h45-13h00 Comp. Session: Lab 3: Study Design in Epidemiology (Tutors, Comp. Lab)
- 13h00-14h00 Lunch
- 14h00-15h30 Comp. Session: Binomial Distribution Tutorial (Tutors, Comp. Lab)
- 15h30-16h00 Free - take a walk!
- 16h00-18h00 Group Work: Project development (Group Breakouts)
- End of Day Questions
Day 4
- 07h45-08h15 Breakfast
- 08h30-09h15 Lecture: Study Design and Analysis, part II: RCT’s (Carl, Main Hall)
- Side reading: CDC on the Tuskegee Experiment, Declaration of Helsinki, Belmont Report
- 09h15-10h30 Comp. Session: Lab 4: Study Design for Clinical Trials (Tutors, Comp. Lab)
- 10h30-11h00 Coffee
- 11h00-12h00 Lecture: Transmission in Finite Populations (Zinhle, Main Hall)
- 12h00-13h00 Group Work: Project development, with progress checkin (Comp. Lab)
- All checkins in the lab. Odd groups check in with Carl, even with Zinhle. Be prepared to show your draft report, slides, and poster.
- Project Groups
- 13h00-14h00 Lunch
- 14h00-15h30 Group Work: Project development
- 15h30-16h00 Free - take a walk!
- 16h00-18h00 Comp. Session: If incomplete: review questions from Lab 4: Study Design for Clinical Trials (Tutors), Tutorial 3: Probability Distributions and Control Structures, and review questions (Tutors, Comp. Lab). Otherwise Project development
- Final Fundamentals Week Quiz (includes Qs from Friday)
Day 5
- 07h45-08h15 Breakfast
- 08h30-09h30 Lecture: Dynamics of vector-borne pathogens (Zinhle, Main Hall)
- 09h30-10h30 Group Work: Final Group Work (Group Breakouts)
- submit slides to Zinhle by 10h30
- 10h30-11h00 Coffee
- 11h00-13h00 Group Work: Practice presentations and feedback (all, Main Hall)
- Aim for: 6 minutes, 3-4 minutes for questions, 3-4 minutes for feedback; max 15 minutes
- Groups: 11h00-11h15 4, 11h15-11h30 1, 11h30-11h45 3, 11h45-12h00 2, 12h00-12h15 5 (with 45 minute buffer for overruns)
- 13h00-14h00 Lunch
- 14h00-15h00 Group Work: Revisions (Group Breakouts)
- 15h00-15h30 Discussion: Review / Preview (Main Hall)
- 15h30-16h00 Free - take a walk!
- 16h00-18h00 Group Work: Optional: re-present + re-feedback. Optional: poster feedback. (Main Hall)
Week 1: Meaningful Modeling of Epidemiological Data (MMED)
Day 0 (Sunday, 15 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
- 0730? whatsapp checkin
- 07h30-08h20 Organizing Session: Registration (Faikah, Lobby)
- 07h45-08h15 Breakfast
- 08h30-09h00 Welcome and Motivation for Workshop (Reshma, Main Hall)
- 09h00-09h45 Discussion: Public health, epidemiology, and models (Carl, Main Hall)
- Notes: Mutono
- 09h45-10h00 MMED roadmap and program overview (Reshma, Main Hall)
- 10h00-10h30 Coffee
- 10h30-11h30 Lecture: Introduction to dynamic modelling of infectious disease I (Reshma, Main Hall)
- Notes: Carl
- 11h30-12h30 Lecture: Introduction to infectious disease data (Seth, Main Hall)
- Notes: Carl
- 12h30-13h00 faculty meeting
- 12h30-14h00 Lunch
- 13h15-13h45 (technical assistance for participants, Comp. Lab
- Led by Carl
- 14h00-15h00 Lecture: Foundations of dynamical modelling (Jonathan, Main Hall)
- This year’s spreadsheet
-
A similar spreadsheet that also implements a stochastic version!
- Notes: Seth the Motivator
- 15h00-15h30 Comp. Session: Dynamical fever exercise (Mutono, Comp. Lab)
- Launch from R prompt with
ICI3D::dynamicalFever()- assisted by Seth, Carl, Jeremy, Martha
- Stanley should relax!
- Launch from R prompt with
- 15h30-16h00 Tea (poster setup, group 1) (Mutono, and Mentors, Main Hall)
- 16h00-17h00 Dynamical fever exercise, cont. (Comp. Lab)
- Dynamical fever summary (Mutono, Comp. Lab)
- 17h00-18h00 Poster session 1 (Main Hall)
- End of Day Questions
- 18h00-18h30 Dinner
- 19h00-20h30 Ice-breaker/Card games (Faikah, Main Hall)
Day 2
- 07h45-08h15 Breakfast
- 0730? whatsapp checkin
- 08h30-09h15 (Hidden) assumptions of simple ODE models (Cari, Main Hall)
- note takers Mutono
- 09h15-10h00 Live Coding: Introduction to model implementation in R (Reshma, Main Hall)
- Resulting Code
- Notes: Carl
- 10h00-10h30 Coffee
- 10h30-11h30 R Tutorials: Lab 1 - ODE Models (Martha, Comp. Lab)
- 11h30-12h30 Thinking about Data (Mutono, and Mentors, Main Hall)
- note takers Seth
- 12h30-14h00 Lunch
- 14h00-15h00 Lecture: Study design (Reshma, Main Hall)
- note takers: Jonathan
- 15h00-17h00 (with tea break) R Tutorials: Lab 4 - study design II & Tutorial 4 - Visualizing Infectious Disease Data (Seth, Reshma, and Mentors, Comp. Lab)
- Study Design Slides
- Visualization Summary
- Lab 3 - study design I may also be of interest, but is an own-time activity
- 15h30-16h00 Tea (poster setup, group 2) (Mutono, and Mentors, Main Hall)
- 17h00-18h00 Poster session 2 (Main Hall)
- End of Day Questions
- 18h00-18h30 Dinner
- 19h00-20h00 Lecture: Guest Lecture: “Mathematical models of vector-borne diseases: from theory to research” Joseph Challenger
- Moderator Jonathan
Day 3
- 07h45-08h15 Breakfast
- 0730? whatsapp checkin
- 08h30-09h30 Lecture: Consequences of heterogeneity and modelling options (Jonathan, Main Hall)
- Notes: Seth
- 09h30-11h00 (with coffee break) Comp. Session: Lab 2 - Consequences of heterogeneity (Jonathan, Comp. Lab)
- Mentors, Seth, Joe, CarL
- Download lab and supplementary functions
- Summary updated (Jonathan)
- 10h00-10h30 Coffee
- 11h00-14h30 (with lunch break) Introduction to models and data: HIV in Harare (Reshma, and Carl, Comp. Lab)
- Notes: Mutono
- Launch from R prompt with
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.
- Additional info: Distributed Delay Models of Survival (Boxcar Models) and example script
- Summary of Harare tutorial (Carl)
- 12h30-13h00 faculty meeting
- 12h30-14h00 Lunch
- 14h30-15h30 Discussion: Formulating research questions (Cari, and Seth, Section 1, Section 2)
- AIMS in main room assisted by Mutono
- Seth somewhere notes by Rehsma
- 15h30-16h00 Tea
- 16h00-17h30 Lecture: Introduction to statistical philosophy (Jonathan, Main Hall)
- note takers: Cari
- 17h30-18h00 Projects: Topic Intro (Seth Main Hall)
- End of Day Questions
- note takers: Mutono
- 18h00-18h30 Dinner
- 19h00-20h00 Optional: Tutorials catch-up (Mentors, Comp. Lab)
- This catch-up is open, but please sign up for future catch-ups
Day 4
- 07h45-08h15 Breakfast
- 0730? whatsapp checkin
- 08h30-10h00 Discussion: Creating a model world to address a research question (Seth, and Mutono, Section 1, Section 2)
- note takers: Cari, Jonathan
- 10h00-10h30 Coffee
- Lab 5 checkin
- 10h30-11h15 Lecture: Introduction to likelihood (Cari, Main Hall)
- note takers: Carl
- 11h15-12h30 Comp. Session: Lab 5 - Introduction to likelihood (Cari, and Mentors, Comp. Lab)
- helping: Jonathan, Seth, mentors
- 12h30-13h00 faculty meeting
- 12h30-14h00 Lunch
- 14h00-15h30 Live Coding: Participatory coding of a dynamical model (Jonathan, Main Hall)
- This years code (past years generally available here)
- note takers: Carl
- 15h30-16h00 Tea
- 16h00-17h00 Lecture: Introduction stochastic simulation models (Reshma, Main Hall)
- note takers: Carii
- Drum on the drums; remind them about assessment
- 17h00-18h00 Discussion: Exercise 1: Stochastic models (Reshma, Comp. Lab)
- Summary
- Support: Mutono, Jonathan, Seth
- 18h00-18h30 Dinner
- End of Day Questions
- 18h30-19h00 Finish Model Diagram
- 19h00-21h00 Social Event: Drumming (Main Hall)
Day 5
- 07h45-08h15 Breakfast
- 0730? whatsapp checkin
- 08h30-10h00 Discussion: Description of proposed model and assumptions (Mutono, Cari, Seth, and Mentors, Section 1, Section 2)
- Telephone!
- note takers: Team, Reshma
- 10h00-10h30 Coffee
- 10h30-11h15 Lecture: Fitting I (Cari, Main Hall)
- note takers: Mutono
- 11h15-12h15 Mentor presentations (Seth, Main Hall)
- We don’t take formal notes here; you are requested to communicate privately with the mentors
- Seth: mention that lunch not served until 12:30
- 12h15-12h45 faculty meeting
- 12h15-13h45 Lunch (note slight shift)
- 13h45-15h00 Comp. Session: Lab 6 - MLE fitting of an SIR model to prevalence data (Seth, Comp. Lab)
- Jonathan, Reshma, CarL, Carii, mentors
- Intro / Summary Slides
- 15h00-15h30 Projects: Topic Qs (Mutono, Main Hall)
- note takers: Jonathan, Seth
- 15h30-16h00 Tea
- 16h00-17h00 Mid-Clinic Feeback session (Faikah, Main Hall)
- End of Day Questions
- 17h00-18h00 Optional catchup session (Comp. Lab)
- Let the mentors know your questions
- NO LATER THAN 1800: Project selection form
- 18h00-18h30 Dinner
- 19h00-21h00 Social Event: Movie Night (Main Hall)
- Project group: work on group assignments possibly calling on experts
Day 6
- 08h00-09h00 Breakfast
- 0730? whatsapp checkin
- 09h00-10h30 Live Coding: Participatory coding for stochastic model (Carl, Main Hall)
- note takers: Reshma
- 10h30-11h00 Coffee
- 11h00-11h30 Projects: Group Assignments (Mutono, Comp. Lab)
- 11h30-12h30 Optional: Tutorials catch-up or Project Group Work (Mentors, Comp. Lab)
- Social Event: Optional: Group Lunch at Kalky’s (costs covered)
- 16h30 post-Kalky’s all hands faculty meeting in E313; beverages provided
- 18h00-18h30 Dinner
Day 7
-
08h00-09h00 Breakfast
-
Social Event: Social Outing: Cape Point National Park; depart 09h00 sharp
-
18h00-18h30 Dinner
Week 2: MMED Project Focus
Day 8 (Monday, 23 June)
- 07h45-08h15 Breakfast
- 08h30-08h45 Discussion: Feedback responses; Review Schedule & goals (Reshma, Main Hall)
- Notes: Seth
- 08h45-09h30 Lecture: Life cycle of a modeling project (Carl, Main Hall)
- note takers: Mutono, Joe
- 09h30-10h00 Group Work: First meeting of project groups (Group Breakouts)
- 10h00-10h30 Coffee
- 10h30-11h30 Introduction to github (Carl, and Mentors, Comp. Lab)
- note takers: Cari
- 11h30-12h30 Group Work: MMED project work (Group Breakouts)
- 12h30-14h00 Lunch
- 14h00-15h30 Lecture: Likelihood fitting and dynamical models II (Seth, Main Hall)
- Notes: Cari, Jonathan
- Announce github practice no need to sign up
- 15h30-16h00 Tea
- 16h00-18h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
- End of Day Questions
- 18h00-18h30 Dinner
- 19h00-20h00 Optional: Github practice and and trouble-shooting / tutorial catch-up (Carl, and Mentors, Comp. Lab)
Day 9
- 07h45-08h15 Breakfast
- 08h30-10h00 Lecture: Introduction to Markov Chain Monte Carlo (MCMC) (Carl, Main Hall)
- Seth, Mutono
- 10h00-10h30 Coffee
- Photo session
- See MMED photo folder (request access if necessary)
- 10h30-11h30 Comp. Session: Lab 7 & Lab 8 MCMC model fitting (Carl, and Mentors, Comp. Lab)
- Cari, Seth, Jonathan
- 11h30-12h30 Group Work: MMED project work (Group Breakouts)
- 12h30-14h00 Lunch
- 14h00-14h45 Lecture: Data management and cleaning (Mutono, Main Hall)
- Notes: Jonathan
- 14h45-15h30 Comp. Session: Tutorial 5: Data cleaning, data (Jeremy, Comp. Lab)
- Summary (Mentors)
- note takers: Mutono, Cari
- 15h30-16h00 Tea
- 16h00-18h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
- End of Day Questions
- 18h00-18h30 Dinner
- 19h00-20h00 Optional: Github Trouble-shooting / tutorial catch-up (Mentors, Comp. Lab)
Day 10
- 07h45-08h15 Breakfast
- 08h30-09h30 Lecture: Model assessment (Jonathan, Main Hall)
- Notes: Joe, Cari
- 09h30-10h00 Group Work: MMED project work (Group Breakouts)
- 10h00-10h30 Coffee
- 10h30-11h00 Group Work: MMED project work (Group Breakouts)
- 11h00-12h30 either Group Work: MMED project work or Live Coding: Analysis pipelines (resulting code) (Carl, Group Breakouts or Main Hall)
- note takers: Carl
- Get a more direct summary title for this
- 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 Guest Lecture: Mmamapudi Kubjane (Main Hall)
Day 11
- 07h45-08h15 Breakfast
- 08h30-10h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
- 10h00-10h30 Coffee
- 10h30-12h30 Group Work: MMED project work (Group Breakouts)
- 12h30-14h00 Lunch
- 14h00-15h30 either Group Work: MMED project work or Live Coding: Participatory coding for study design and simulation based validation (Jonathan, Main Hall)
- Code
- note takers: Carl
- One-study code; Many-study code
- 15h30-16h00 Tea
- 16h00-17h30 Discussion: Modelling for policy (Seth, Main Hall)
- note takers: Jonathan
- 18h00-18h30 Dinner
- 19h00-20h00 MMED project work
Day 12
- 07h45-08h15 Breakfast
- 08h30-12h30 Group Work: MMED project work (Group Breakouts)
- 10h00-10h30 Coffee
- 12h30 Report due
- 13h00 Presentations due
- 12h30-13h30 Lunch
- 13h30-15h30 Group Work: Project presentations (Mutono, Main Hall)
- note takers: Jonathan
- 15h30-16h00 Tea
- 16h00-17h00 Discussion: Feedback session II (Faikah, Main Hall)
- 17h15-17h45 Closing Remarks (Reshma, Main Hall)
- note takers: TBD
- 18h00-18h30 Dinner