Clinic Schedule

Sunday

Interactive session 1a (dushoff)

• Please join the session by 16:25. We will begin promptly at 16:30.
• 16:30-16:55 Welcome and some logistics (bolton)
  • Faculty introductions; introduce DAIDD glossary
• 16:55-17:10 What are we doing here? (vanschalkwyk) UPDATE linking system Slide folder
• 17:15-17:45 Data, models, and science (reiner)
  • Lecture handouts; Draft slides
• 17:45-18:00 Working with the DAIDD technical tools (li, bruce) (15 mins)
  • Release form?
  • ICI3D R package
  • Make sure your slides are uploaded for the next session!
• 18:00-18:30 Ice breakers (bruce)
  • use this as a chance to introduce some Teams features - silly questions and getting to know you stuff; switch rooms midway through

Interactive session 1b (mthombothi)

• 19:30-21:30 Research pitches
  • Order of introductions
  • Allow for 15 minute break
• 21:30-22:00 Faculty meeting

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 bellan
  • Plan forward links: dynamics PICO acronym, more time for SIR foundation
  • Consider updating the video/create new video
• Video lecture: Introduction to model worlds pulliam
  • Reference: Bellan et al. 2015
  • Reference: Kucharski et al. 2015
• Exercise: Formulating research questions for modeling projects Also available in the Assignments folder in the General Channel of the DAIDD Participants Team
• 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.
• • FB updated link to DAIDD 2023

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty

Monday

Interactive session 2a (vanschalkwyk)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

Do we need a Monday recap? Historically no.

• 16:30-16:50 Summary and questions: Intuitive aspects of dynamics and introduction to model worlds (are)
  • Summary should be about individual session 1 videos
• 16:50-17:00 Overview of research plan development and structure (vanschalkwyk) (10 mins?) - Overview of research plan development and structure
• https://www.dropbox.com/s/5lojjt5yqjsw668/DAIDD2022guide.pdf?dl=1 NB this is the 2022 link.
• 17:00-18:30 Tutorial: Dynamical Fever - computer exercise and discussion (bolton and all faculty)
  • Leader needs to control time in both directions; groups should know what should be discussed in each portion
  • Let’s make sure to discuss the first set of questions before getting into the second set of simulations
  • To get started, run the following command at the R Studio command line (after installing the ICI3D package):

ICI3D::dynamicalFever

Interactive session 2b (mwangi)

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-20:00 Discussion: Dynamical Fever (bolton) model description, modeling terminology, and the DAIDD glossary - Download the taxonomy NOTE (30 mins?)
• 20:00-21:30 Small group session: research questions for modeling projects (all faculty) NOTE (90 mins)
  • Step-by-step guide
• 21:30-22:00 Faculty meeting

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
• Dushoff double check and decide whether to change it
  • Intro (from live workshop)
  • Discussion
  • Lecture handouts; Draft slides
• Video lecture: Modeling in practice: The life cycle of a modeling project, from conception to publication (reiner)
• Video lecture: optional Integration of Data and Models for schistosomiasis control (deleo)
  • Part 1; Part 2; Part 3
• Video lecture optional: Omicron Modelling Session at Epidemics8 conference, December 2021
  • Enter passcode: 9JKhQ&=Y
  • (pulliam, pearson, Sheetal Silal)

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty

Tuesday

Thumbi is not availabe on Tuesday Zi is not available 17h30-19h30 SAST

Interactive session 3a (bolton)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

• 16:30-16:45 Daily recap (mthombothi) (15 mins)For Interactive Session 2a/b
  • DAIDD roadmap slideset - recap folder
• 16:45-17:00 Summary and discussion: The SIR model family (dushoff)
• 17:00-17:30 Exercise: Building an SIR model from scratch (dushoff) (30 mins?) NOTE + 5 min stretch break
  • 2022 live spreadsheet (copy or save to work on it)
  • Spreadsheet with stochastic code
• 17:30-17:45 Summary and discussion: The life cycle of a modeling project (reiner)
• 17:45-18:30 Live lecture: The simplest model (pearson) Slide folder, Source for slides NOTE (45 mins)
  • Google sheet NOTE Formerly: Simple individual-based models

Interactive session 3b (reiner)

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-20:15 Exercise: Simple individual-based models (li) (30 mins)
  • To get started, run the following command at the R Studio command line (after installing the ICI3D package):
  • lengthened by 15 minutes for logistical reasons 2022

ICI3D::reedFrost

• 20:15-21:30 Exercise: Creating a model world to address a research question (mwangi)
• ((vanschalkwyk/mwangi)) (90 mins)
  • shortened by 15 minutes for logistical reasons 2022
• 21:30-22:00 Faculty meeting

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 Pulliam
  • Research question: What level of vaccination is necessary to eliminate domestic dog rabies in Tanzania?
  • Check with Thumbi if we can upload last year’s video
• Video lecture: Stochastic simulation models (borchering) borchering
  • Introduction
  • Part 1
  • Part 2
  • Where are the slides?
• Video lecture: Heterogeneity, contact patterns, and modeling options (dushoff)
  • Lecture handouts; Draft slides
  • Exercise summary

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty

Wednesday

Interactive session 4a (are)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

• 16:30-16:45 Daily recap (kubjane) (15 mins)
• 16:45-17:00 Summary and discussion: Stochastic simulation models (mthombothi) (15 mins)
• 17:00-18:30 Small-group session: matching models to questions (all faculty) (90 minutes)

Interactive session 4b (li)

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-19:45 Summary and discussion: Impact of contact patterns, consequences of heterogeneity, and modeling options (dushoff) (15 mins)
• 19:45-20:30 Tutorial: Heterogeneity in disease emergence (reiner, bolton, are) (45 mins)
  • To get started, run the following command at the R Studio command line (after installing the ICI3D package):
  • TODO make this a link!

ICI3D::heterogeneityTutorial

• 20:30-21:30 Mid-session feedback (bruce) (60 mins)
• Mid-session post-mortem:

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 (scott)
  • Part 1
  • Part 2
  • Part 3
  • Part 4
• Video lecture optional: Seasonality and Infectious Diseases (deleo)
  • Part 1
  • Part 2
  • Part 3
• Video lecture optional: Introduction to statistical philosophy (dushoff)
• Video lecture optional: Faculty research presentation: The potential for cervical cancer elimination in South Africa (vanschalkwyk) Catch-up on earlier materials, as needed

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty
• Zi not available for Tea

Thursday

Interactive session 5a (dushoff)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

• 16:30-16:50 Regroup after feedback (vanschalkwyk) (20 mins)
• 16:50-17:05 Daily recap (mhlanga) (15 mins)
• 17:05-17:20 Summary and discussion: Models and data: introduction to model fitting (vanschalkwyk) (15 mins)
• 17:20-18:30 Writing exercise: description of proposed model and assumptions (mthombothi) (65 mins?) Model telephone
  • practice diagram, description
  • instructions for in-person version

Interactive session 5b (mthombothi)

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-21:00 Tutorial: Model fitting (are) (90 mins?) - Tutorial notes
  • (Tutorial wrapup by dushoff) - Boxcar Model Slides
  • To get started, run the following command at the R Studio command line (after installing the ICI3D package):

ICI3D::hivTutorial

• 21:00-21:30 Review: model taxonomy (bolton) Set up ‘planning your approach exercise’
  • Planning document
• 21:30-22:00 Faculty meeting

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 bruce to make folders for assignments
  • 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 (dushoff)
  • This video needs to be re-edited! Why did nobody tell me‽
    • Look around minute 24!
  • Handouts and slides are in Teams slide folder
• 2022 link Possible social activity (Game night) - eg, from c. 21:30 JD will bring beer; JP will source games

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty

Friday

Interactive session 6a (vanschalkwyk)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

• 16:30-16:45 Daily recap (mhlanga) (15 mins)
• 16:45-17:00 Summary and discussion: Model evaluation and comparison (dushoff) (20 mins?)
• 17:00-18:30 Live lecture: Modelling to inform policy: Modelling the South African adult TB epidemic: Exploring the effects of HIV, sex differences, and assessing the impact and cost-effectiveness of TB programme interventions (kubjane)
  • Onchocerciasis (nyamai) what is up with this link??
  • Onchocerciasis (Mutono Nyamai)
  • OLD: Slides, Related papers: Flasche et al. 2016, Hladish et al. 2016 NOTE (85 mins?)

Interactive session 6b (vanschalkwyk)

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-20:00 Live lecture: Model-based inference and the bigger picture (reiner) (30 mins)
  • Need to update this lecture!
  • Slides (by Bellan)
  • Kucharski et al. Ebola paper
  • Camacho Ebola paper
  • Bellan HIV paper
• 20:00-20:30 Review and Discussion (Moderator: vanschalkwyk) (30 mins free form discussion / Q&A on topics raised by participants)
• 20:30-21:30 Small group session: planning your approach (all faculty) (60 mins)
• 21:30-22:00 Faculty meeting

Individual session 6

Please complete the following between the end of Friday’s interactive session and the beginning of Saturday’s interactive session.

• 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: COVID-19: from pandemic to endemic? Vaccination, reopening & evolution in highly vaccinated settings (Faculty research presentation) (are)
• Video lecture optional: Use of models in public health decision-making II: COVID-19 Scenario Modeling Hub Webinar (Faculty research presentation) (borchering)
• Does this need to be updated?
• Current link is apparently to Becky et al. (MIDAS)
  • [Slides] NOTE update link!
  • Slides, Reference: Bellan et al. (2015) Lancet Inf Dis, Ebola Papers by ICI3D Faculty
• Video lecture optional: Modelling to inform policy: Polio (mthombothi)

• Video lecture optional: Modelling to inform policy: Elimination of transmission of onchocerciasis with Ivermectin mass drug administraton with or without vector control in sub-Saharan Africa (nyamai) Special session (North America) 22:00-23:30

• One-on-one mentoring sessions
  • Schedule to be posted
  • [Schedule] NOTE update link!

Reminder:

• 0:30 Tea with North American Faculty
• 13:30 Tea with African Faculty
• Zi not available for Tea

Saturday

Individual session 7

Special session (Africa) 15:00-16:30

• One-on-one mentoring sessions with Bolton, Mwangi, Cari, and Zinhle NOTE Schedule to be posted
  • [Schedule] NOTE update link!

Interactive session 7a (are)

16:30-18:30 SAST / 14:30-16:30 BST / 9:30-11:30 EST / 6:30-8:30 PST

• 16:30-16:45 Daily recap (li) (15 mins)
• 16:45-18:30 Discussion of research plans/proposals (Moderator: are)
  • Proposal order

Interactive session 7b

19:30-21:30 SAST / 17:30-19:30 BST / 12:30-14:30 EST / 9:30-11:30 PST

• 19:30-21:00 Final feedback session (bruce) (60-90 mins)
• 21:00-21:15 Closing session (vanschalkwyk) (15 mins)