Course Materials

E²M²:  Ecological and Epidemiological Modeling in Madagascar

January 13-20, 2018 + January 22, 2018

Centre ValBio, Ranomafana National Park, Madagascar

Syllabus

Sat, Jan 13:

  • 6:30am: Depart from Tana (MICET office in Manakambahiny) via bus, travel to Ranomafana (lunch stop Antsirabe)
  • 6:30-7:30pm: Dinner
  • 7:30-8:15pm: Introduction and Road Map: What are we doing here? (Cara)
  • 8:15-9:00pm: Ice Breakers (Cara)

Sun, Jan 14: “Thinking About Data” 

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-9:30am: Lecture: Models and Data (Tanjona)
  • 9:30-10:30am: Software installation and catch-up
  • 10:30am – 11:00am: Break
  • 11:00am – 12:00pm:  Lecture/Tutorial: Exploring & visualizing data in R (Christian)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: 1-min student introductions and research presentations (Cara)
  • 2:00-3:00pm: Tutorial: Revisit four intro tutorials from prep (all)
  • 3:00-6:00pm: Hike in Ranomafana National Park (all)
  • 6:30-7:30pm: Dinner
  • 8:00-9:00pm: Instructor research presentations (Jess, Calistus)

Mon, Jan 15: “Thinking About Data (continued)”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-10:00am:Lecture: Linear regression, mixed models, and simple statistics (Andres)
  • 10:00-10:30pm: Break
  • 10:30am-12:00pm: Tutorial: Basic statistical modeling in R (Andres)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Writing Exercise: Formulating research questions (HW) (Cara)
  • 2:00-3:00pm: Lecture: PIVOT’s Role in E2M2 (Matt)
  • 3:00-6:00pm: One-on-one mentor sessions (all)
  • 8:00-9:00pm: Instructor research presentations (Cara, Christian)

Tues, Jan 16: “Thinking About Mechanism”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-10:00am: Lecture: Introduction to Compartmental Models and Differential Equations (Jess)
  • 10:00-10:30am: Break
  • 10:30am-12:00pm: Tutorial: Building Mechanistic Models in R (Jess)
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Small group session: Refining research questions for modeling (Cara)
  • 2:30-3:00pm: Writing Exercise: Creating a model world to address a research question (HW for tomorrow) (Cara)
  • 3:00-3:30pm: Break
  • 3:30-5:00pm: Exercise + Discussion: Dynamical Fever (Calistus + Christian)
  • 5:00-6:00pm: Instructor research presentations (Jess, Calistus)
  • 6:30-7:30pm: Dinner
  • 8:00-10:00pm: Night hike in Ranomafana National Park (all)

Wed, Jan 17: “Fitting Models to Data”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-9:30am: Lecture w/Tutorial: Model Fitting in Practice – the Basic Concept (Cara)
  • 9:30-10:00am: Break
  • 10:00-11:00am: Exercise: Epidemics Cards (Cara + Calistus)
  • 11:00am-12:00pm: Tutorial: Model Fitting with Epidemic Cards (Cara)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Tutorial: Model Fitting in Spreadsheet Form (Cara)
  • 2:00pm-3:00pm: Lecture: Alternative Approaches to Model Fitting (Calistus)
  • 3:00-3:30pm: Break
  • 3:30-5:00pm: Model Telephone with Model Diagrams (Tanjona)
  • 6:30-7:30pm: Dinner
  • 8:00-9:00pm: Mentor + faculty research presentations (Mentor, Tanjona)

Thurs, Jan 18: “Refining Your Work”

  • 6:30-8:00am: Breakfast
  • 8:00-11:00am: Group hike in Ranomafana National Park
  • 11:00am-12:00pm: Group Journal Club: Discussion of a scientific article (Tanjona)
  • 12:00pm-1:00pm: Lunch
  • 1:00-2:00pm: Lecture: Modeling Extensions – Metapopulation Theory, Incorporating Heterogeneity, etc. (Tanjona)
  • 2:00-3:00pm: Tutorial: Model Fitting and Comparison with Age-Prevalence Data (Cara)
  • 3:00-3:30pm: Break
  • 3:30-6:30pm: Work/Free time: Final Research Plans
  • 6:30-7:30pm: Dinner
  • 8:00-9:00pm: Optional social activity. TBA

Fri, Jan 19: “Putting it all in Perspective”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-9:30am: Lecture: Model Evaluation and Comparison (Calistus)
  • 9:30-10:00am: Break
  • 10:00-11:00am: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
  • 11:00am-12:00pm: Lecture: Wrapping up – how far have we come? (Cara)
  • 12:00-1:00pm: Lunch
  • 1:00pm – 4:30pm: Research plan work time (all)
  • 3:00-3:30pm: Break
  • 4:30-5:30pm: Final feedback session (Julio)
  • 6:30-7:30pm: Dinner
  • 7:30pm onwards: Farewell party

Sat, Jan 20:

  • 6:30-8:00am: Breakfast
  • 8:00-9:00am: pack up and board bus
  • Return to Antananarivo via bus

Mon, Jan 22:

  • 9:00-11:00am: Closing ceremony and final student presentations (Cara)