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 (Institut Pasteur) via bus, travel to Ranomafana (lunch stop Antsirabe)
  • 6:30-7:30pm: Dinner
  • 7:30-8:30pm: Introductions and Road Map: What are we doing here? (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.
      • Mentors + instructors make sure all students have the proper materials installed and work through 4 tutorials with them
  • 10:30am – 11:00am: Break
  • 11:00am-12:00pm: 1-min student introductions and research presentations (Cara)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm Lecture: Exploring & visualizing data in R (Christian + Cara)
  • 2:00-3:00pm: Tutorial: Exploring & visualizing data in R (Christian + Cara)
  • 3:00-3:30pm: Break
  • 3:30pm-4:30pm: Lecture: Linear regression and simple statistics (Andres)
  • 4:30-5:30pm: Tutorial: Basic statistical modeling in R (Andres)
  • 5:30-6:30pm: Free time
  • 6:30-7:30pm: Dinner

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

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30am-9:30am: Lecture: Introduction to mixed modeling (Andres)
  • 9:30am-10:00am: Break
  • 10:00am-11:00am: Tutorial: Mixed modeling in R (Andres)
  • 11:00am-12:00pm: Writing Exercise: Formulating research questions (HW) (Cara)
  • 12:00pm-1:00pm: Lunch
  • 1:00-2:30pm: Lecture w/Tutorial: Introduction to occupancy modeling (Fidy)
  • 2:30-3:00pm: Prep for hike
  • 3:00-6:30pm: Afternoon hike in Ranomafana National Park
  • 6:30-7:30pm: Dinner

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
  • 1:00-3:00pm: Small group session: Refining research questions for modeling (Cara introduces + all instructors lead small groups)
  • 3:00-3:30pm: Writing Exercise: Creating a model world to address a research question (HW for tomorrow) (Cara)
  • 3:30-4:00pm: Break
  • 4:00-6:00pm: Exercise + Discussion: Dynamical Fever (Calistus + Christian)
  • 6:30-7:30pm: Dinner
  • 8:00-9:00pm: Mentor research presentations (Jean-Marius, Ornella, Antso)

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
  • 1:00pm-2:00pm: Lecture: Alternative Approaches to Model Fitting (Calistus)
  • 2:00-3:30pm: Model Telephone with Model Diagrams (Tanjona)
  • 3:30-4:00pm: Break
  • 4:00-5:00pm: Lecture: PIVOT’s Role in E2M2 (Matt)
  • 5:00-6:30pm Mid-session feedback
  • 6:30-7:30pm: Dinner

Thurs, Jan 18: “Refining Your Work”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda (Cara)
  • 8:30-9:30am:  Lecture: Modeling Extensions – Metapopulation Theory, Incorporating Heterogeneity, etc. (Tanjona)
  • 9:30-10:00am: Break
  • 10:00-11:30am: Lecture w/Tutorial: Introduction to Network Modeling (Fidy)
  • 11:30am-12:00pm: Final research plans (HW) (Cara)
  • 12:00pm-1:00pm: Lunch
  • 1:00pm-2:00pm: Lecture: Introduction to Spatial Modeling (Amy)
  • 2:00-4:00pm: Tutorial: Spatial Modeling and Statistics in R (Amy)
  • 4:00-4:30pm: Break
  • 4:30-6:30pm: Work time + one-on-one mentoring sessions (all)
  • 6:30-7:30pm: Dinner

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
  • 10:00am-11:30am: Tutorial: Model Selection with Age-Prevalence Data (Cara)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
  • 2:00-3:00pm: Lecture: Looking back: How far have we come? (Calistus)
  • 3:00-4:30pm: Research plan work time + mentoring sessions (all)
  • 4:30pm onwards: Afternoon off and farewell dinner in Ranomafana town

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:

  • 9:00-10:30am: Closing ceremony and final student presentations (Cara)