Clinic Schedule

This is an archived version of the schedule from the DAIDD 2022 clinic (December 2022, Microsoft Teams). Some links may not work at this time.

Sunday

Interactive session 1a ((vs))

• Please join the session by 16:25. We will begin promptly at 16:30.
• 16:30-16:45 Welcome and some logistics ((dushoff))
• 16:45-17:10 What are we doing here? ((pulliam)) 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 ((hladish), (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
• 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
• 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.

Reminder:

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

Monday

Interactive session 2a ((hladish))

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 ((deleo))
  • CHECK
• 16:50-17:00 Overview of research plan development and structure ((pulliam)) (10 mins?) - Overview of research plan development and structure
• 17:00-18:30 Tutorial: Dynamical Fever - computer exercise and discussion ((li) 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 ((pulliam))

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 ((vs)) 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
  • 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: 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

Interactive session 3a ((li))

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)
  • 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 ((hladish)) 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 ((hladish)) (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 ((vs)) (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?
• Video lecture: Stochastic simulation models (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 ((pulliam))

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 ((brown)) (15 mins)
• 16:45-17:00 Summary and discussion: Stochastic simulation models ((dushoff)) (15 mins)
• 17:00-18:30 Small-group session: matching models to questions (All faculty) (90 minutes)

Interactive session 4b ((deleo))

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), (li), (pulliam)) (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: ~ 21:30 NOTE CvS and JP will not have power from 20:00 - 22:30 but will join by phone

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: 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 ((vs))
• Catch-up on earlier materials, as needed

Reminder:

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

Thursday

JP giving a seminar; need to sort out timing; will otherwise be available CP not available Thursday AM; shouldn’t be a problem

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 ((vs)) (20 mins)
• 16:50-17:05 Daily recap ((are)) (15 mins)
• 17:05-17:20 Summary and discussion: Models and data: introduction to model fitting ((dushoff)) (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 ((li)) (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 ((pulliam)) 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
  • This video needs to be re-edited! Why did nobody tell me‽
    • Look around minute 24!
  • Handouts and slides are in Teams slide folder

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 ((vs))

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 ((brown)) (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:
  • Polio ((pulliam), (mthombothi))
  • 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 ((mthombothi))

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 ((dushoff)) (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: (li)) (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.

• Video lecture: Faculty Research Lecture ((tbd))
  • Was Larisse
• 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) ((tbd))
  • 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

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

Saturday

Individual session 7

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

• One-on-one mentoring sessions with Bolton, Mwangi, Pearson, and Pulliam NOTE Schedule to be posted
  • Schedule NOTE update link!

Interactive session 7a

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 ((are)) (15 mins)
• 16:45-18:30 Discussion of research plans/proposals (Moderator: (vs))
  • 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 ((dushoff)) (15 mins)