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

• R-Bootcamp is a one-day optional session held at Institut Pasteur de Madagascar in Antananarivo, which we offer as a resource for students who need to brush up on programming skills prior to the start of the formal course.

• 8:00-8:30am: Brief Introductions (Tanjona Ramiadantsoa)
• 8:30-9:30am: Lecture: Intro to R Studio (Tanjona Ramiadantsoa)
• 9:30-10:00am: Small Groups: Software installation and catch-up. Mentors + instructors make sure all students have the proper materials installed and work through the Intro Tutorials. (Tanjona Ramiadantsoa, Christian, Mentors)
• 10:00-10:30am: Coffee Break
• 10:30am-11:30am: Tutorial: Intro to R Studio (Tanjona Ramiadantsoa, with help from Mentors)
  • Includes:
    • Knowing your working environment
    • Assigning variables
    • Basic arithmetic
    • Running a script
• 11:30-1:00pm: Lunch + extra time if certain students need extra time for downloads/installations.
• 1:00-2:00pm: Lecture: Exploring & visualizing data in R (Christian)
• 2:00-3:00pm : Tutorial: Exploring & visualizing data in R (Christian, with help from Santino)
• 3:00-3:30pm: Coffee Break
• 3:30-4:00pm: Lecture: Intro to for-loops, if-else statements, and functions (Cara Brook)
• 4:00-4:30pm: Tutorial: Intro to for-loops, if-else statements, and functions (Cara Brook)
• 4:30-5:30pm: Open mentoring session for outstanding questions or continued work on tutorials from above or from homework (All instructors + mentors)

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”

• 6:30-8:00am: Breakfast
• 8:00-8:30am: Brief Introductions
• 8:30-10:00am: Lecture: Data and Models (Cara)
• 10:00-10:30am: Coffee Break
• 10:30am-12:00pm: Introductions: 3-min student introductions
• 12:00-1:00pm: Lunch
• 1:00-3:00pm: Formulating research questions (Cara)
  • For HW, write your own research question
• 3:00-3:30pm: Coffee Break
• 3:30-5:00pm: Lecture/Tutorial: Linear Regression and Simple Statistics (Andres)
• 6:30-7:30pm: Dinner

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)
  • Please read ‘Model-Guided Field Work’ by Restif et al. 2012. prior to coming to class and be prepared to discuss
• 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)
  • All students should have a workable statistical and mechanistic question by the end of the session
  • For HW, ‘Creating a Model World + Building a Statistical Framework’, will be due on Wednesday, Dec 14
• 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)
  • Read “Prioritizing COVID-19 vaccination efforts and dose allocation within Madagascar” by Rasambainarivo et al. prior to coming to class and be prepared to discuss
• 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)
  • Meet out front of CVB!

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”

• 6:30-8:00am: Breakfast
• 8:00-8:15am: Road Map and Daily Agenda
• 8:15-9:30am: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
• 9:30-10:00am: Coffee Break
• 10:00am-11:45am: C4C student presentations (6 students at 15 min each)
• 11:45am-12:00pm: Group photo - Wear your E²M² shirts!
• 12:15-1:15pm: Lunch
• 1:15-1:45pm: Lecture: Looking back: How far have we come? (Cara)
• 1:45-3:00pm: One-on-One Student-Instructor Meetings (All Instructors)
• 3:00-6:30pm: Work time + free time in town (All Instructors)
• 6:30-9:00pm: Farewell dinner in Ranomafana town (Hotel Manja)
• 9:30pm: Return bus to CVB

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:
  • Spatial Visualization and Plotting
  • Occupany Modeling

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