2022 Syllabus
Please follow instructions for installing packages in R here.
Please download this folder of sequences to your personal computer prior to departing Antananarivo.
Instructors on duty for C4C student help can be found here.
Friday, Dec 9: Intro to R Bootcamp
Saturday, Dec 10: “Travel Day”
- 5:30am: Meet at Institut Pasteur for departure to Ranomafana (lunch stop Ambositra)
- 6:30-7:30pm: Dinner
- 7:30-9:00pm: Introductions
Sunday, Dec 11: “Getting Started with the Basics”
Monday, Dec 12: “Using Models with Data”
- 6:30-8:00am: Breakfast
- 7:45-8:45am: C4C students present their projects to instructors (E2M2 students do not need to attend)
- 8:45-9:00am: Road Map and Daily Agenda
- 9:00-10:15am: Lecture/Tutorial: Model Guided Study Design (Cara)
- 10:15-10:45am: Coffee Break
- 10:45am-12:00pm: Lecture: Introduction to Compartmental Models (Sophia)
- 12:00-1:00pm: Lunch
- 1:00-2:30pm: Tutorial: Building Mechanistic Models in R (Sophia)
- 2:30-3:00pm: Coffee Break
- 3:00-3:30pm: Large Group Session: Refining research questions for modeling (All Instructors)
- Refine questions from yesterday and develop statistical frame work + model diagram
- 3:30-5:30pm: Small Group Sessions: Refining research questions for modeling (All instructors lead small groups)
- 6:30-7:30pm: Dinner
Tuesday, Dec 13: “Applying Simple Models”
- 6:30-8:00am: Breakfast
- 8:00-10:00am: Exercise + Discussion: Dynamical Fever (Gwen, Sophia, Santino)
- 10:00-10:30am: Coffee Break
- 10:30am-12:00pm: Work time + One-on-One Student-Instructor Meetings (All Instructors)
- Students should fully develop their Statistical Frameworks and Model Diagrams by the end of today
- 12:30-1:00pm: Lunch
- 1:30-3:00pm: Lecture/Tutorial: Introduction to Mixed Modeling (Andres)
- 3:00-3:30pm: Coffee Break
- 3:30-4:30pm: Small Group Discussion: Reading a Research Paper (Christian + Michelle)
- 4:30-5:30pm: Mid-Session Feedback (Santino)
- Students, please complete this form before midnight tonight. Santino will also solicit feedback on these topics directly.
- 6:30-7:30pm: Dinner
- 7:00pm: Night walk Ranomafana National Park (optional)
Wednesday, Dec 14: “Fitting Models to Data”
- 6:30-8:00am: Breakfast
- 7:30-11:00am: Morning hike in Ranomafana National Park
- Meet out front of CVB! Get your breakfast early
- 11:00-11:30am: Coffee Break
- 11:30am-12:45am: Lecture/Tutorial: Model Fitting in Practice – the Basic Concept (Michelle)
- 12:45-2:00pm: Lunch
- 2:00-2:20pm: Response to Feedback & Review ‘Creating a Model World + Building a Statistical Framework’. Now due on Thursday, Dec 15
- 2:20-3:00pm: Exercise: Epidemic Cards (Gwen, Sophia, Santino)
- 3:00-3:30pm: Coffee Break
- 3:30-4:30pm: Tutorial: Model Fitting with Epidemic Cards (Gwen, Sophia, Santino)
- 4:30-6:00pm: One-on-One Student-Instructor Meetings (All Instructors)
- 6:30-7:30pm: Dinner
Thursday, Dec 15: “Refining Your Work + Bells and Whistles”
- 6:30-8:00am: Breakfast
- 8:00-8:05am: Road Map, Daily Agenda
- 8:05-9:30am: Activity: Model Telephone with Model Diagrams (Cara)
- Example model description here.
- 9:30-10:15am: Lecture + Activity: So many models! How to choose?!? (Cara)
- 10:15-10:45am: Coffee Break
- 10:45am-12:00pm: Lecture/Tutorial: Model Selection and Comparison (Christian)
- 12:00-1:00pm: Lunch
- 1:00-2:30pm:Lecture/Tutorial: Introduction to Phylogenetic Modeling (Gwen)
- 2:30-3:00pm: Coffee Break
- 3:00-4:00pm Lecture/Tutorial: Introduction to Network Models (Michelle)
- 4:00-4:15pm: Final research plans (HW) (Cara)
- Due on Wednesday, January 4, 2023 at midnight! Submit here.
- 4:15-4:45pm: Research Snapshots (Gwen, Cara, Sophia)
- 4:45-6:00pm: C4C students practice presentations with instructors
- Work time/free time for E2M2 students
- 6:30-7:30pm: Dinner
Friday, Dec 16: “Putting It All In Perspective”
Saturday, Dec 17: (Travel Day)
- 5:30-6:00am: Breakfast to go
- 6:00am: Board bus
- Return to Antananarivo
Please submit your responses to our Final Feedback form here by midnight on Monday, December 19, 2022.
- Note: We will not be teaching a few specific lessons this year, but here are links to the lectures/tutorial to peruse on your own time if interested:
Wednesday, January 4, 2023: Work day at Madagascar Biodiversity Center
- 8:00am-4:00pm: Sophia (in the morning) and Cara (in the early mornining and afternoon) will be available to answer questions and help with presentation preparation at Madagascar Biodiversity Center at Tsimbazaza.
Thursday, Thursday, January 5 2023
- 2:00-4:30pm: Final Symposium and presentations at Institut Pasteur du Madagascar
- 4:30-5:30pm: Informal reception