Clinic Schedule
Sunday
Interactive session 1a
- Please join the session by 06:25. We will begin promptly at 06:30.
- 06:30-06:45 Welcome and some logistics (Juliet Pulliam)
- 06:45-07:10 What are we doing here? (Juliet Pulliam)
- 07:15-07:45 Data, models, and science (Jonathan Dushoff)
- 07:45-08:00 Working with the DAIDD technical tools (Carl Pearson)
- Make sure your slides are uploaded for the next session!
- 08:00-08:30 Ice breakers (Faikah Bruce)
Interactive session 1b
- 09:30-11:30 Research pitches (Moderator: Becky Borchering)
Individual session 1
Please complete the following between the end of Sunday’s interactive session and the beginning of Monday’s interactive session.
- Video lecture: Introduction to Infectious Disease Modelling
- Video lecture: Introduction to model worlds
- Reference: Bellan et al. 2015
- Reference: Kucharski et al. 2015
- Exercise: Formulating research questions for modeling projects
- Recommended reading: If you have not already read the compiled pre-assigned readings, please do so now. These and other optional readings are available through the Pre-readings Folder in the DAIDD Participants Team.
Reminder:
- 14:30 Tea with North American Faculty
- 01:00 Tea with African Faculty
- 00:30 (optional)
Monday
Interactive session 2a
- 06:30-06:50 Summary and questions: Intuitive aspects of dynamics and introduction to model worlds (Becky Borchering)
- 06:50-07:00 Overview of research plan development and structure (Juliet Pulliam)
- 07:00-08:30 Tutorial: Dynamical Fever - computer exercise and discussion (Larisse Bolton and all faculty)
- To get started, run the following command at the R Studio command line (after installing the ICI3D package):
ICI3D::dynamicalFever()Interactive session 2b
- 09:30-10:00 Discussion: Dynamical Fever (Larisse Bolton)
- 10:00-11:30 Small group session: research questions for modeling projects (All faculty)
Individual session 2
Please complete the following between the end of Monday’s interactive session and the beginning of Tuesday’s interactive session.
- Exercise: Finalize your research question and post to the Research Questions channel.
- Video lecture: The SIR model family - conceptual framework and introduction to difference and differential equations
- Video lecture: Modeling in practice: The life cycle of a modeling project, from conception to publication
- Video lecture: Omicron Modelling Session at Epidemics8 conference, December 2021
- Enter passcode: 9JKhQ&=Y
- Video lecture (optional): Faculty research presentation (Pulliam on COVID) - _select at least one from the following list:
Reminder:
- 14:30 Tea with North American Faculty
- 03:30 Tea with African Faculty
Tuesday
Interactive session 3a
- 06:30-06:45 Daily recap (Becky Borchering)
- 06:45- 07:00 Summary and discussion: The SIR model family (Jonathan Dushoff)
- 2021 live spreadsheet (copy or save to work on it)
- Spreadsheet with stochastic code
- 07:00-07:30 Exercise: Building an SIR model from scratch (Jonathan Dushoff)
- 07:30-07:45 Summary and discussion: The life cycle of a modeling project ((reiner))
- 07:45-08:30 Live lecture: The simplest model (Carl Pearson)
Interactive session 3b
- 09:30-10:00 Exercise: Simple individual-based models (Carl Pearson)
- To get started, run the following command at the R Studio command line (after installing the ICI3D package):
ICI3D::reedFrost()- 10:00-11:30 Exercise: Creating a model world to address a research question ((mwangi))
Individual session 3
Please complete the following between the end of Tuesday’s interactive session and the beginning of Wednesday’s interactive session.
- Exercise: Creating a model world assignment.
- Step-by-step guide
- Upload your initial model diagram before Wednesday’s interactive session (DAIDD Participants > General > Files > 04_modelDiagram > 04.1_InitialDiagrams).
- Video (optional): Creating a model world - another example
- Research question: What level of vaccination is necessary to eliminate domestic dog rabies in Tanzania?
- Video lecture: Stochastic simulation models
- Introduction
- Part 1
- Part 2
- Slides on Teams - to be added
- Video lecture: Heterogeneity, contact patterns, and modeling options (Jonathan Dushoff)
Reminder:
- 14:30 Tea with North American Faculty
- 03:30 Tea with African Faculty
Wednesday
Interactive session 4a
- 06:30-06:45 Daily recap ((li))
- 06:45-07:00 Summary and discussion: Stochastic simulation models (Becky Borchering)
- 07:00-08:30 Small-group session: matching models to questions (All faculty)
Interactive session 4b
- 09:30-09:45 Summary and discussion: Impact of contact patterns, consequences of heterogeneity, and modeling options (Jonathan Dushoff)
- 09:45-10:30 Tutorial: Heterogeneity in disease emergence (Jonathan Dushoff, Carl Pearson, (li))
- To get started, run the following command at the R Studio command line (after installing the ICI3D package):
ICI3D::heterogeneityTutorial()- 10:30-11:30 Mid-session feedback (Faikah Bruce)
Individual session 4
Please complete the following between the end of Wednesday’s interactive session and the beginning of Thursday’s interactive session.
- Exercise: Update your model diagram and post to Teams before Thursday’s interactive session (DAIDD Participants > General > Files > 04_modelDiagram > 04.2_UpdatedDiagrams).
- Video lecture: Models and data: introduction to model fitting
- Video lecture: Faculty research presentation ((de leo))
- Video lecture (optional): Introduction to statistical philosophy (Jonathan Dushoff)
- Video lecture (optional): Faculty research presentation (John Hargrove)
- Catch-up on earlier materials, as needed
Reminder:
- 14:30 Tea with North American Faculty
- 03:00 Tea with African Faculty
Thursday
Interactive session 5a
- 06:30-06:50 Regroup after feedback (Juliet Pulliam)
- 06:50-07:05 Daily recap ((mwangi))
- 07:05-07:20 Summary and discussion: Models and data: introduction to model fitting (Larisse Bolton)
- 07:20-08:30 Writing exercise: description of proposed model and assumptions ((reiner))
Interactive session 5b
- 09:30-11:00 Tutorial: Model fitting ((li))
- To get started, run the following command at the R Studio command line (after installing the ICI3D package):
ICI3D::hivTutorial()- 11:00-11:30 Review: model taxonomy (Juliet Pulliam)
Individual session 5
Please complete the following between the end of Thursday’s interactive session and the beginning of Friday’s interactive session.
- Exercise: Finalize your model diagram and description and post to Teams
- Place them both as a single file in DAIDD Participants > General > Files > 05_modelDescription
- Now would also be a good time to review the research plan instructions
- Exercise: Work through the document for planning your approach (available in DAIDD Participants > General > Files > Assignments)
- Video lecture: Model evaluation and comparison
- Handouts and slides are in Teams slide folder https://stellenbosch.sharepoint.com/:f:/r/sites/DAIDD2021Participants224/Shared%20Documents/General/Slides?csf=1&web=1&e=c6mcKs
- Lecture handouts
- Draft slides
Reminder:
- 14:30 Tea with North American Faculty
- 03:00 Tea with African Faculty
Friday
Interactive session 6a
- 06:30-06:45 Daily recap ((reiner))
- 06:45-07:00 Summary and discussion: Model evaluation and comparison (Jonathan Dushoff)
- 07:00-08:30 Live lecture: Use of models in public health decision-making (Faculty research presentation) - Now with more COVID! (Carl Pearson)
Interactive session 6b
- 09:30-10:00 Live lecture: Model-based inference and the bigger picture (Jonathan Dushoff)
- 10:00-10:30 Review and Discussion (Moderator: (mwangi))
- 10:30-11:30 Small group session: planning your approach (All faculty)
Individual session 6
Please complete the following between the end of Friday’s interactive session and the beginning of Saturday’s interactive session.
- Video lecture: Faculty Research Lecture (Larisse Bolton)
- Writing exercise: revise based on feedback and plan for moving forward (including identified resources and potential collaborators)
- Submit your final research plan via Teams
- Submit your final slide via teams
- Include your research question and model diagram on a single page in a PDF document
- Video lecture (optional): Use of models in public health decision-making II: COVID-19 Scenario Modeling Hub Webinar (Faculty research presentation) (Becky Borchering)
Special session: 12:00-13:30
- One-on-one mentoring sessions with Borchering, Dushoff, Li, de Leo, and Reiner
Reminder:
- 14:30 Tea with North American Faculty
- 03:00 Tea with African Faculty
Saturday
Individual session 7
Special session: 02:00-03:30
- One-on-one mentoring sessions with Bolton, Mwangi, Pearson, and Pulliam
Interactive session 7a
- 06:30-06:45 Daily recap ((li))
- 06:45-08:30 Discussion of research plans/proposals (Moderator: Jonathan Dushoff)
Interactive session 7b
- 09:30-11:00 Final feedback session (Faikah Bruce)
- 11:00-11:15 Closing session (Juliet Pulliam)