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.

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 (Fidy)
  • 8:30-9:30am: Lecture: Intro to R Studio (Fidy)
  • 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 Intro Tutorial. (Fidy, Christian, Mentors)
  • 10:00-10:30am: Coffee Break
  • 10:30am-11:30am: Tutorial: Intro to R Studio (Fidy, 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
  • 3:30-4:30pm: Lecture/tutorial: Intro to for-loops, if-else statements, and functions (Fidy)
  • 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”

  • 6:00am: 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: Models and Data (Cara)
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Introductions: 2-min student introductions
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Formulating research questions (Cara)
    • For HW, write your own research question
  • 2:30-3:00pm: 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
  • 8:00-8:30am: Road Map and Daily Agenda
  • 8:30-10:00am: Lecture/Tutorial: Model Guided Study Design (Cara)
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture: Introduction to Compartmental Models (Sophia)
    • Lecture should introduce terms and review concepts of stochastic/deterministic model and discrete/continuous time
  • 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, assign: ‘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: Morning hike in Ranomafana National Park
  • 10:00-10:30am: Coffee Break
  • 10:00am-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
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Exercise + Discussion: Dynamical Fever (Gwen, Sophia, Santino)
  • 2:30-3:30pm: Lecture/Tutorial: Introduction to Mixed Modeling (Andres)
  • 3:30-4:00pm: Coffee Break
  • 4:00-5:00pm: Small Group Discussion: Reading a Research Paper (Christian + Michelle)
  • 5:00-6:00pm: Mid-Session Feedback (Santino)
  • 6:30-7:30pm: Dinner

Wednesday, Dec 14: “Refining Your Work”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda, and Response to Feedback
  • 8:15-9:30am: Lecture w/Tutorial: Model Fitting in Practice – the Basic Concept (Michelle)
  • 9:30-10:30am: Exercise: Epidemic Cards (Gwen, Sophia, Santino)
  • 10:30-11:00am: Coffee Break
  • 11:00am-12:00pm: Tutorial: Model Fitting with Epidemic Cards (Gwen, Sophia, Santino)
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Lecture/Tutorial: Model Selection and Comparison (Christian)
  • 2:30-3:00pm: Coffee Break
  • 3:00-4:00pm: Model Telephone with Model Diagrams (Cara)
  • 4:00-6:00pm: One-on-One Student-Instructor Meetings (All Instructors)
  • 6:30-7:30pm: Dinner
  • 8:00pm: Night walk Ranomafana National Park (optional)

Thursday, Dec 15: “Bells and Whistles”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map, Daily Agenda
  • 8:15-10:00am: Lecture/Tutorial: Introduction to Phylogenetic Modeling (Gwen)
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture/Tutorial: Introduction to Spatial Visualization and Plotting (Sophia)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Activity: The Metapopulation Game (Cara)
  • 2:00-2:30pm: Lecture/Tutorial: Modeling Insights from the Metapopulation Game (Cara)
  • 2:30-3:00pm: Coffee Break
  • 3:00-4:00pm Lecture/Tutorial: Introduction to Network/Occupancy Modeling/GAMs (Michelle)
  • 4:00-4:30pm: Final research plans (HW) (Cara)
  • 4:30-5:00pm: Research Snapshots (All Instructors)
  • 5:00-6:30pm: Work time + C4C students practice presentations with instructors
  • 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-12:00pm: C4C student presentations (7 students at 15 min each)
  • 11:15am-11:45am: Lecture: Looking back: How far have we come? (Cara)
  • 11:45am-12:00pm: Group photo - Wear your E2M2 shirts!
  • 12:00-1:00pm: Lunch
  • 1:00-6:30pm: Work time + one-on-one student-instructor meetings (All Instructors)
  • 6:30-9:00pm: Farewell dinner in Ranomafana town (Hotel Manja)
  • 9:30pm: Return bus to CVB

Saturday, Dec 17: (Travel Day)

  • 5:00-6:00am: Breakfast to go
  • 6:00am: Board bus
  • Return to Antananarivo

Final Symposium from 2-4:30pm on Thursday, January 4 2023 at Institut Pasteur du Madagascar

  • Students will have the opportunity to present their work in a final symposium in January 2023 at Institut Pasteur de Madagascar in Antananarivo. Participation in this symposium is optional, based on students’ availability and is not required.