2020 Syllabus

Please follow instructions for installing packages in R here.

Saturday, Jan 4: ‘R Bootcamp’ (attendance optional) (at Institut Pasteur de Madagascar in Antananarivo)

  • 8:00-8:30am: Brief Introductions (Fidy, Cara, Tanjona)
  • 8:30-9:30am: Lecture: Intro to R Studio (Fidy)
  • 9:30-10:30am: 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)
  • 10:30-11:00am: Coffee Break
  • 11:00am-12:30pm: Tutorial: Intro to R Studio (Fidy, with help from Mentors)
    • Includes:
      • Knowing your working environment
      • Assigning variables
      • Basic arithmetic
      • Running a script
  • 12:30-1:30pm: Lunch + extra time if certain students need extra time for downloads/installations.
  • 1:30-2:30pm: Lecture: Exploring & visualizing data in R (Christian)
  • 2:30-3:00pm: Coffee Break
  • 3:00-5:00pm: Tutorial: Exploring & visualizing data in R (Christian, with help from Mentors)

Sunday, Jan 5: ‘R Bootcamp’ (attendance optional)

Monday, Jan 6: “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 and Ice Breakers (Mentors)

Tuesday, Jan 7: “Understanding Your System”

Wednesday, Jan 8: “Building Simple Models”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda
  • 8:15-9:30am: Lecture/Tutorial: Lecture: Linear Regression and Simple Statistics (Fara)
  • 9:30-10:00am: Coffee Break; prep for hike
  • 10:00am-12:00pm: Morning hike in Ranomafana National Park
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Lecture/Tutorial: Introduction to Compartmental Models (Cara)
  • 2:30-3:00pm: Coffee Break
  • 3:00-4:30pm: Exercise + Discussion: Dynamical Fever (Christian, Fara, Mentors)
  • 4:30-6:30pm: Small Group Sessions: Refining research questions for modeling (all instructors lead small groups)
  • 6:30-7:30pm: Dinner

Thursday, Jan 9: “More Complicated Models”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda (Cara)
  • 8:15-10:00am: Lecture/Tutorial: Introduction to Mixed Modeling (Andres)
  • 10:00-10:30am: Coffee Break
  • 10:30-12:00pm: Live Coding + Tutorial: Building Mechanistic Models in R (Cara)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Activity: The Metapopulation Game (Tanjona)
  • 2:00-2:30pm: Lecture: Modeling Insights from the Metapopulation Game (Tanjona)
  • 2:30-3:30pm: Model Telephone with Model Diagrams
    • Example model description is available here (Cara)
  • 3:30-4:00pm: Coffee Break
  • 4:00-5:30pm: Work time + One-on-One Student-Instructor Meetings (All Instructors)
  • 5:30-6:30pm: Mid-session feedback (Christian)
  • 5:30-6:30pm: Mentors practice presentations with instructors. Students do not need to attend.
  • 6:30-7:30pm: Dinner

Friday, Jan 10: “Refining Your Work”

Saturday, Jan 11: “Putting It All In Perspective”

Sunday, Jan 12: (Travel Day)

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

Monday, Jan 13

  • IPM Salle de Direction is open with WiFi connections for students to upload documents. We will have 1-2 instructors and 1-2 mentors on hand for office hourse to answer questions if students need help.
  • Please upload your final slide presentations here by midnight on Monday, January 13, 2020!

Tuesday, Jan 14: “Sharing Your Work” (at Institut Pasteur de Madagascar in Antananarivo)

  • 9:00-11:00am: Closing ceremony and final student presentations
  • 11:00am-12:00pm: Final Feedback Session
  • 12:30-2:00pm: Farewell lunch
  • 2:00-4:30pm: Mini-symposium: “Modeling Insights Into Ecology and Epidemiology” (Instructor presentations)
  • 4:30pm: Social Hour