Clinic on Dynamical Approaches to Infectious Disease Data

The twelfth annual DAIDD clinic ~ December 10–16, 2023 ~ Virtual Edition

  1. Schedule
  2. DAIDD 2023

Clinic Schedule

Select your timezone:

Sunday

Interactive session 1a (dushoff)

  • Please join the session five minutes in advance. We will begin promptly.
  • Welcome and some logistics (bolton)
    • Faculty introductions; introduce DAIDD glossary
  • What are we doing here? (vanschalkwyk) UPDATE linking system Slide folder
  • Data, models, and science (reiner)
  • 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!
  • 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)

Individual session 1

Please complete the following between the end of Sunday’s interactive session and the beginning of Monday’s interactive session.

  • Tea with North American Faculty

Monday

  • Tea with African Faculty

Interactive session 2a (vanschalkwyk)

Do we need a Monday recap? Historically no.

  • Summary and questions: Intuitive aspects of dynamics and introduction to model worlds (are)
    • Summary should be about individual session 1 videos
  • 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.
  • 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)

Individual session 2

Please complete the following between the end of Monday’s interactive session and the beginning of Tuesday’s interactive session.

  • Tea with North American Faculty

Tuesday

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

  • Tea with African Faculty

Interactive session 3a (li)

Interactive session 3b (reiner)

  • 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()
  • Exercise: Creating a model world to address a research question (mwangi)
  • ((vanschalkwyk/mwangi)) (90 mins)
    • shortened by 15 minutes for logistical reasons 2022
  • 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.

  • Tea with North American Faculty

Wednesday

  • Tea with African Faculty
  • Zi not available for Tea

Interactive session 4a (are)

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

Interactive session 4b (li)

  • Summary and discussion: Impact of contact patterns, consequences of heterogeneity, and modeling options (dushoff) (15 mins)
  • Tutorial: Heterogeneity in disease emergence (reiner, 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()
  • 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.

  • Tea with North American Faculty

Thursday

  • Tea with African Faculty
  • Zi not available for Tea

Interactive session 5a (dushoff)

  • Regroup after feedback (vanschalkwyk) (20 mins)
  • Alert all participants to the deadline to upload. They will be alllocated in groups accordingly - based on whether they submitted.
  • FB to allocate based on those who have submitted - update! update! update!
  • Daily recap (mhlanga) (15 mins)
  • Summary and discussion: Models and data: introduction to model fitting (vanschalkwyk) (15 mins)
  • Writing exercise: description of proposed model and assumptions (mthombothi) (65 mins?) Model telephone

Interactive session 5b (mthombothi)

  • 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()

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
    • See Notation notes__ on the Resources page
    • 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
  • Tea with North American Faculty

Friday

  • Tea with African Faculty
  • Zi not available for Tea

Interactive session 6a (vanschalkwyk)

  • Daily recap (mhlanga) (15 mins)
  • Summary and discussion: Model evaluation and comparison (dushoff) (20 mins?)
  • 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)

Interactive session 6b (vanschalkwyk)

Individual session 6

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

Special session (North America) 22:00-23:30

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

Individual session 7

  • There will not be a tea session today

Saturday

  • There will not be a tea session today
  • Zi not available for Tea

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

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

Interactive session 7a (are)

  • Daily recap (li) (15 mins)
  • Discussion of research plans/proposals (Moderator: are)

Interactive session 7b

  • Final feedback session (bruce) (60-90 mins)
  • Closing session (vanschalkwyk) (15 mins)