Clinic Schedule

This is an archived version of the schedule from the MMED 2018 clinic.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.

Sunday, 27 May

• 17:00 – 18:00 Registration and welcome, AIMS lobby
• 18:00 – 18:30 Dinner, AIMS Dining Hall

Monday, 28 May

• 8:00 – 8:25 Registration and welcome, AIMS lobby
  • Please gather in the main lecture hall by 8:30.
• 8:30 – 9:00 Welcome and Motivation for Workshop (Juliet Pulliam, Zinhle Mthombothi, and John Hargrove)
• 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models (Eduard Grebe)
• 10:00 – 10:30 Coffee break
• 10:30 – 10:45 Organizational session: MMED Road Map and programme overview (Juliet Pulliam)
• 10:45 – 11:30 Lecture: Introduction to Thinking About Data I (Brian Williams)
• 11:30 – 12:30 Lecture: Introduction to dynamic modeling of infectious diseases (Juliet Pulliam)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • If you plan to use your laptop for the 15:00 computer exercise, Eva and Carl will help you get set up at 12:30 in the main lecture hall.
• 14:00 – 15:00 Parallel sessions
  • Track A: Introduction to infectious disease data (Faikah Bruce)
  • Track B: Foundations of dynamic modeling (Jonathan Dushoff)
• 15:00 – 15:30 Exercise and discussion: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: Eva Ujeneza)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 16:50 Exercise and discussion: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: Eva Ujeneza)
• 16:50 – 17:00 Discussion: Dynamical Fever and Model Worlds (Juliet Pulliam)
• 17:00 – 18:00 Poster session I
• 18:00 – 18:30 Dinner
• 19:00 – 19:30 Social Activity: Ice breakers
• 19:30 – 20:30 Social Activity: Card games: Bullsh!t and Casino

Tuesday, 29 May

• 8:30 – 9:15 Lecture: (Hidden) assumptions of simple ODE models (Juliet Pulliam)
• 9:15 – 10:00 Live coding session: Introduction to model implementation (Carl Pearson)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Computer Session: R Tutorials - Lab 1: ODE models in R (with Jonathan Dushoff, Reshma Kassanjee, Juliet Pulliam, Eva Ujeneza, Roger Ying); MedPH break-out group (Rebecca Borchering, Zinhle Mthombothi)
  • All R tutorials and labs are linked from this page
  • You should have completed R Tutorials I-III prior to the Clinic. If you have not previously used R, we suggest you review these tutorials during this session, as the material they cover form the foundation for the computer sessions throughout the workshop. Please use this opportunity to ask any questions you may have regarding the material in these tutorials.
  • When you have completed Lab 1 (required), you may take a break or move on to Tutorial 4: Visualizing Infectious Disease Data in R (recommended)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 14:45 Parallel sessions (Note: for this session only, Track A participants may attend the Track B session.)
  • Track A: Lecture: Introduction to Thinking About Data II (John Hargrove)
  • Track B: Lecture: Basic stochastic simulation models (Rebecca Borchering)
• 14:45 – 15:30 Parallel sessions
  • Track A: Computer Session: R Tutorials - Lab 1: ODE models in R (as needed), and Tutorial 4: Visualizing Infectious Disease Data in R (with Faikah Bruce, Reshma Kassanjee, Thumbi Mwangi, Eva Ujeneza)
  • Track B: Computer Session: R Tutorials - Lab 1: ODE models in R (as needed), and Exercise 1: Basic stochastic simulation models (with Rebecca Borchering, Zinhle Mthombothi, Carl Pearson, Roger Ying)
  • Exercise 1 Summary (Rebecca Borchering)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 16:50 Computer Session: R Tutorials continued (Faikah Bruce, Reshma Kassanjee, Zinhle Mthombothi, Thumbi Mwangi, Eva Ujeneza)
• 16:50 – 17:00 Discussion:
  • Lab 1 Summary (Zinhle Mthombothi)
  • Tutorial 4 Summary (Reshma Kassanjee)
• 17:00 – 18:00 Poster session II
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional guest lecture): Florian Marx

Wednesday, 30 May

• 8:30 – 9:15 Lecture: Consequences of heterogeneity, and modeling options (Jonathan Dushoff)
• 9:15 – 10:15 Computer Session: R Tutorials - Lab 2: Consequences of heterogeneity (with Jonathan Dushoff, Rebecca Borchering, Thumbi Mwangi, Eva Ujeneza, Roger Ying)
  • Lab 2 Summary (Roger Ying)
• 10:15 – 10:30 Coffee break
• 10:30 – 10:45 Sunshine break
• 10:45 – 11:00 Lecture: Introduction to models and data: HIV in Harare (John Hargrove)
• 11:00 – 12:30 Computer Session: Harare data in groups of <4 (with John Hargrove, Reshma Kassanjee, Zinhle Mthombothi,Juliet Pulliam, Brian Williams)
  • To run the tutorial, first load the ICI3D R package (require('ICI3D')), then load the tutorial (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) - Slides (Juliet Pulliam)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • Please fill in the weekend activities form! (Due by 13:00 on Wed 30 May.).
• 14:00 – 14:30 Computer Session: Harare/other data in same groups (with Rebecca Borchering, John Hargrove, Thumbi Mwangi, Brian Williams, Roger Ying)
• 14:30 – 15:30 Discussion: Harare tutorial (John Hargrove)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Parallel sessions
  • Track A: Formulating Research Questions A (Juliet Pulliam)
  • Track B: Formulating Research Questions B (Rebecca Borchering)
• 17:00 – 18:00 Poster session III
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional guest lecture): Guest lecture (Jacky Snoep)

Thursday, 31 May

• 8:30 – 10:00 Parallel sessions
  • Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology: Where does modeling fit? (Faikah Bruce) and R Tutorials - Lab 3: Study Design in Epidemiology (with Faikah Bruce, Reshma Kassanjee, Thumbi Mwangi, John Hargrove, Eva Ujeneza)
  • Lab 3 Summary (Eva Ujeneza)
  • Track B: Exercise: Creating a model world to address a research question (Juliet Pulliam) - Slides, Assignment and examples
• 10:00 – 10:30 Coffee break
• 10:30 – 12:00 Lecture: Introduction to statistical philosophy (Jonathan Dushoff)
• 12:00 – 12:30 Discussion: MMED research projects (Rebecca Borchering)
  • Potential project groups
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Lecture: Participatory coding of a dynamical model (Carl Pearson, with Juliet Pulliam)
• 15:30 – 16:00 Tea
• 16:00 – 16:45 Lecture: Introduction to Likelihood (Eva Ujeneza)
• 16:45 – 18:00 Computer Session: R Tutorials - Lab 5: Introduction to Likelihood Lab (with Jonathan Dushoff, Zinhle Mthombothi, Carl Pearson, Eva Ujeneza, Roger Ying)
  • Lab 5 Summary (Carl Pearson)
• 18:00 – 18:30 Dinner
• 19:30 – 21:00 Social activity: Drumming

Friday, 1 June

• 8:30 – 10:00 Parallel sessions:
  • Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology II: RCT’s (Carl Pearson) - R Tutorials - Lab 4: Study Design for Clinical Trials (with Rebecca Borchering, Faikah Bruce, Reshma Kassanjee, Thumbi Mwangi, Carl Pearson)
  • Dataset for Lab 4
  • Lab 4 Summary (Faikah Bruce)
  • Track B: Exercise: Description of proposed model and assumptions (Juliet Pulliam)
• 10:00 – 10:30 Coffee break
• 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Juliet Pulliam)
• 11:15 - 12:30 Computer Session: Lab 6: MLE fitting of an SIR model to prevalence data (with Jonathan Dushoff, Zinhle Mthombothi, Carl Pearson, Juliet Pulliam, Roger Ying)
  • Additional info: Parameter transformation - Slides
  • Lab 6 Summary (Juliet Pulliam)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • Please fill in this form to indicate what you will work on during the tutorial catch-up session on Saturday and whom you would like to meet for a mentoring session next week. (Due by 17:00 on Friday 1 June.)
• 14:00 – 15:30 Mentor presentations (Reshma Kassanjee, Zinhle Mthombothi, Thumbi Mwangi, Roger Ying; Moderator: Jonathan Dushoff)
• 15:30 – 16:00 Tea
• 16:00 – 17:00 MMED Projects (Moderator: Juliet Pulliam)
  • Project group sign-up will be available after this session
• 17:00 – 18:00 Mid-session Feedback (Moderator: Gavin Hitchcock)
• 18:00 – 18:30 Dinner
• 19:30 – 21:30 Social Activity: Movie night (Outbreak)

Saturday, 2 June

• 9:00 – 10:30 Lecture: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture (Jonathan Dushoff)
• 10:30 – 11:00 A good chance to sign up for project groups and Coffee break
• 11:00 – 12:30 Computer Session: Tutorial catch-up, as needed (with Faikah Bruce, Reshma Kassanjee, Thumbi Mwangi, Carl Pearson, Roger Ying)
• 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
• 14:00 – Free/working afternoon

Sunday, 3 June

• Free day – optional group trip to Cape Point
  • We will leave at 10:00. Please meet in the AIMS lobby by 9:55.

Monday, 4 June

• 8:30 – 9:15 Lecture: Doing Science (Brian Williams)
• 9:15 – 9:30 Organizational Session: Schedule and goals for the second week (Rebecca Borchering)
• 9:30 – 10:00 Work Session: Project groups meet for the first time (All instructors)
• 10:00 – 10:30 Coffee break
• 10:30 – 11:30 Computer Session: Introduction to GitHub (Eduard Grebe) (with Zinhle Mthombothi, Thumbi Mwangi, Carl Pearson, Eva Ujeneza)
• 11:30 – 12:30 Work Session: Work plans for group projects (Project groups)
• 14:00 – 15:30 Lecture: Likelihood fitting and dynamic models II (Pearson)
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session (Project groups)
  • 16:30 – 17:30 Mentoring Session: See assignments
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 GitHub practice and troubleshooting (Pearson) (with Kassanjee, Mthombothi, Mwangi, Ying)

Tuesday, 5 June

• 8:30 – 10:00 Lecture: Introduction to Monte Carlo Markov Chains (MCMC) (Carl Pearson)
• 10:00 – 10:30 Coffee break
• 10:30 - 11:30 Computer session: MCMC fitting Labs 7-8 in R Tutorials (with Jonathan Dushoff, Eduard Grebe, Reshma Kassanjee, Carl Pearson, Roger Ying)
  • Lab 7 Summary (Eduard Grebe)
• 11:30 – 12:30 Work Session (Project groups); MedPH break-out group (Rebecca Borchering, Zinhle Mthombothi)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 14:45 Lecture: Data wrangling I: Data management and cleaning (Jonathan Dushoff)
• 14:45 – 15:30 Computer session: R Tutorials - Tutorial 5: Data cleaning (recommended) (with Jonathan Dushoff, Reshma Kassanjee, Thumbi Mwangi, Juliet Pulliam, Eva Ujeneza)
  • Tutorial 5 Summary (Thumbi Mwangi)
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session (Project groups)
  • 16:30 – 17:30 Mentoring Session: See assignments
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 AIMS Public Lecture Series (optional): Jonathan Dushoff

Wednesday, 6 June

• 8:30 – 9:30 Lecture: Model assessment (Jonathan Dushoff) - Slides to be added
• 9:30 - 10:00 Computer Session: Tutorial catch-up, as needed (with Faikah Bruce, Rebecca Borchering, Zinhle Mthombothi, Eduard Grebe, Roger Ying)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Work Session (Project groups)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • Sign up to go to on Saturday’s field trip by 13:00.
• 14:00 – 15:30 Work Session (Project groups)
  • 14:00 – 14:45 Optional Lecture: Stochastic modelling IIA (Jonathan Dushoff)
  • 14:45 – 15:30 Optional Live Coding Session: Stochastic modelling IIB (Carl Pearson)
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session (Project groups)
  • 16:30 – 17:30 Mentoring Session: See assignments
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional guest lecture): Guest lecture (Cari van Schalkwyk)

Thursday, 7 June

• 8:30 – 9:15 Lecture: A decision tree for vaccine trial design during public health emergencies (work from the WHO Blueprint for Research & Development) (Jonathan Dushoff) - Slides
• 9:15 - 10:00 Computer Session: Tutorial catch-up, as needed (Eduard Grebe, Reshma Kassanjee, Thumbi Mwangi, Carl Pearson, Eva Ujeneza)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Work Session (Project groups) - Mentors
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Work Session (Project groups)
  • 14:00 – 14:30 Optional Lecture: Data wrangling IIA (Eduard Grebe)
  • 14:30 – 15:00 Optional Live Coding Session: Data wrangling IIB (Carl Pearson)
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session (Project groups)
  • 16:30 – 17:30 Mentoring Session: See assignments
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Work session (Project groups)

Friday, 8 June

• 8:30 – 9:15 Discussion: Modeling for policy (Brian Williams)
• 9:15 – 10:00 Work Session (Project groups)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Work Session (Project groups)
  • 10:30 – 11:30 Mentoring Session: See assignments
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Final presentations
• 15:30 – 16:00 Tea
• 16:00 – 17:00 Final Feedback Session (Moderator: Gavin Hitchcock)
• 17:30 – Closing session
• 18:00 – 18:30 Dinner
• 20:00 – 22:00 Social Activity: Card games

Saturday, 9 June

Note: Breakfast at AIMS will be served from 7:45 to 8:15.

• Clinic officially ends on Friday, but there will be an optional group trip on Saturday.