Clinic on Meaningful Modeling of Epidemiological Data

The eighth annual MMED clinic ~ May 29 - June 9, 2017 ~ Muizenberg, Cape Town, South Africa

  1. MMED 2017
  2. Schedule

Clinic Schedule

The MMED 2017 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, 28 May

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

Monday, 29 May

  • 8:00 – 8:25 Registration and welcome, AIMS lobby
    • If you have a laptop, please see Jan in the IT office (Room 110) during registration to get set up with wifi access.
    • Please gather in the main lecture hall by 8:30.
  • 8:30 – 9:00 Welcome and Motivation for Workshop (Green, Pulliam, and Hargrove)
  • 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models (Scott) - Slides
  • 10:00 – 10:30 Coffee break
  • 10:30 – 10:45 Organizational session: MMED Road Map and programme overview (Pulliam)
  • 10:45 – 11:30 Lecture: Introduction to Thinking About Data I (Hargrove) - Slides
  • 11:30 – 12:30 Lecture: Introduction to dynamic modeling of infectious diseases (Bellan) - Slides
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
    • If you still need wifi access, please see Jan in the IT office (Room 110) between 13:30 and 14:00 to get this set up.
    • If you plan to use your laptop for the 15:00 computer exercise, Cari and Juliet will help you get set up at 12:30 in the main lecture hall.
  • 14:00 – 15:00 Parallel sessions
  • 15:00 – 15:30 Exercise and discussion: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: van Schalkwyk)
  • 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: van Schalkwyk)
  • 16:50 – 17:00 Discussion: Dynamical Fever and Model Worlds (Pulliam) - Slides
  • 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, 30 May

  • 8:30 – 9:15 Lecture: (Hidden) assumptions of simple ODE models (Pulliam) - Slides
  • 9:15 – 10:00 Lecture: Introduction to model implementation (Dushoff) - Live coding example
  • 10:00 – 10:30 Coffee break
  • 10:30 – 12:30 Computer Session: R Tutorials - Lab 1: ODE models in R (with Dushoff, Gershom, Green, Ngonghala, Pulliam); MedPH break-out group (Borchering, 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 (Scott) - Slides
    • Track B: Lecture: Basic stochastic simulation models (Borchering) - Slides
  • 14:45 – 15:30 Parallel sessions
  • 15:30 – 16:00 Tea and poster set-up
  • 16:00 – 16:50 Computer Session: R Tutorials continued (Green, Mthombothi, Ngognghala, Scott) & Mentoring session (from 15:45)
  • 16:50 – 17:00 Discussion:
  • 17:00 – 18:00 Poster session II
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Real-world example (optional lecture): Research Talks (Sheetal Silal, Reshma Kassanjee)

Wednesday, 31 May

  • 8:30 – 9:15 Lecture: Consequences of heterogeneity, and modeling options (Dushoff) - Slides - Handouts
  • 9:15 – 10:15 Computer Session: R Tutorials - Lab 2: Consequences of heterogeneity (with Bellan, Borchering, Dushoff, Gershom, Mthombothi) - Summary (Gershom) - Slides
  • 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 (Hargrove)
  • 11:00 – 12:30 Computer Session: Harare data in groups of <4 (with Hargrove, Gershom, Green, Mthombothi, Pulliam, Williams)
    • You will need the most recent version of the ICI3D R package for this tutorial. If you are using your laptop for the tutorials, please update the package before you begin by running the command devtools::install_github('ICI3D/ici3d-pkg') in R studio.
    • 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
  • 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • 14:00 – 14:30 Computer Session: Harare/other data in same groups. (with Borchering, Green, Gershom, Ngonghala, van Schalkwyk)
  • 14:30 – 15:30 Discussion: Harare data and spreadsheet work (Hargrove) - Slides
  • 15:30 – 16:00 Tea and poster set-up
  • 16:00 – 17:00 Parallel sessions
  • 17:00 – 18:00 Poster session III
  • 18:00 – 18:30 Dinner
  • 19:30 – 21:00 Social activity: Drumming

Thursday, 1 June

Friday, 2 June

  • 8:30 – 10:00 Parallel sessions - Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology II: RCT’s (Scott) - Slides - R Tutorials - Lab 4: Study Design for Clinical Trials (with Bellan, Gershom, Mthombothi, Scott, van Schalkwyk)
  • 10:00 – 10:30 Coffee break
  • 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Pulliam) - Slides
  • 11:15 - 12:30 Computer Session: Lab: MLE fitting of an SIR model to prevalence data (with Bellan, Borchering, Green, Mthombothi, Pulliam)
    • Additional info: Parameter transformation - Slides
    • Lab Summary (Mthombothi) - Slides to be added
  • 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.
  • 14:00 – 15:30 Mentor presentations (Buri Gershom, Kathleen Green, Zinhle Mthombothi; Moderator: Dushoff)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:00 MMED Projects (Moderator: Dushoff)
    • Project group sign-up will be available after this session
  • 17:00 – 18:00 Mid-session Feedback (Moderator: Hitchcock)
  • 18:00 – 18:30 Dinner
  • 19:30 – 21:30 Social Activity: Movie night (Perfect Sense)

Saturday, 3 June

  • 9:00 – 9:45 Lecture: A decision tree for vaccine trial design during public health emergencies (work in progress from the WHO Blueprint for Research & Development) (Bellan) - Slides
  • 9:45 – 10:30 Computer Session: Tutorial catch-up, as needed (with Dushoff, Gershom, Green, Ngonghala, Scott)
  • 10:30 – 11:00 A good chance to sign up for project groups and Coffee break
  • 11:00 – 12:30 Lecture: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture (Bellan) - Code on Tutorials page
  • 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
  • 14:00 – Free/working afternoon

Sunday, 4 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, 5 June

Tuesday, 6 June

Wednesday, 7 June

  • 8:30 – 10:00 Reading Session (Williams)
    • To be read in advance (spend 1 hour total on this):
      • Spend 45 minutes reading Williams et al. 2017
      • Spend 15 minutes reading Korenromp 2015
      • Reading Questions: When reading the above two papers, please try to identify how their assumptions about the following differ:
        1. antiretroviral treatment (ART) efficacy
        2. antiretroviral treatment (ART) coverage
        3. risk heterogeneity
    • Additional references for use during the session: UNAIDS 2016,
  • 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. (You will need to be logged into GitHub to sign up.)
  • 14:00 – 15:30 Work Session (Project groups)
  • 15:30 – 16:00 Tea
  • 16:00 – 17:30 Work Session (Project groups)
  • 18:00 – 18:30 Dinner
  • 19:00 – 20:00 Note that the research talk has been rescheduled for Thursday due to the storm.

Thursday, 8 June

Friday, 9 June

  • 8:30 – 10:00 Work Session (Project groups)
  • 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.)
  • 14:00 – 15:45 Final presentations
  • 15:45 – 16:00 Tea
  • 16:05 – 17:05 Final Feedback Session (Moderator: Hitchcock)
  • 17:15 – 17:45 Closing session
  • 18:00 – 18:30 Dinner
  • 21:00 – 23:00 Social Activity: TBD

Saturday, 10 June

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