2018 Syllabus

E2M2class

Please follow instructions for installing packages in R here.

Follow along with R tricks posted through the week here.

Sat, Jan 13: (Travel)

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
1:00-3:00pm Lecture/Tutorial: Exploring & visualizing data in R (Christian)
3:00-3:30pm: Break
3:30-5:30pm: Lecture/Tutorial: Linear regression and simple statistics (Andres)
5:30-6:30pm: Free time
6:30-7:30pm: Dinner

Mon, Jan 15: “Deeper Thinking About Data”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda (Cara)
8:15am-9:45am: Lecture/Tutorial: Introduction to mixed modeling (Andres)
9:45 - 10:00am: Coffee Break. Prep for hike!
10:00am-1:00pm: Morning walk in Ranomafana National Park
1:00pm-2:00pm: Lunch
2:00 - 3:00pm: Writing Exercise: Formulating research questions (HW) (Cara)
3:00-3:30pm: Break
3:30-5:00pm: Lecture/Tutorial: Introduction to occupancy modeling (Fidy)
5:00-6:30pm: Free time, or one-on-one mentoring
6:30-7:30pm: Dinner

Tues, Jan 16: “Thinking About Mechanism”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda (Cara)
8:15-10:15am: Lecture/Tutorial: Introduction to Compartmental Models and Differential Equations (Jess)
10:15-10:45am: Break
10:45am-12:00pm: Group exercise: Refining research questions for modeling (Cara)
12:00-1:00pm: Lunch
1:00-2:00pm: Small group session: Refining research questions for modeling (cont.) (all instructors lead small groups)
2:00-2:15pm: Writing Exercise: Creating a model world to address a research question (HW) (Cara)
2:15-2:45pm: Break
2:45-4:30pm: Exercise + Discussion: Dynamical Fever (Mentors: Jean-Marius, Ornella, Antso)
4:30-6:00pm: Mid-session feedback (Julio)
6:00 - 6:30pm: Free time
6:30-7:30pm: Dinner

Wed, Jan 17: “Fitting Models to Data”

6:30-8:00am: Breakfast
7:00-8:00am: Mentoring as needed
8:00-8:30am: Road Map and Daily Agenda (Cara)
8:30-10:30am: Lecture/Tutorial: Model Fitting in Practice – the Basic Concept (Cara)
10:00-10:30am: Break
10:30-12:00pm: Exercise: Epidemics Cards (Cara + Amy)
12:00-1:00pm: Lunch
1:00pm-2:00pm: Tutorial: Model Fitting with Epidemic Cards (continued from above) (Amy)
2:00-3:30pm: Model Telephone with Model Diagrams (Mentors: Jean-Marius, Ornella, Antso)
3:30-4:00pm: Break
4:00-5:00pm: Lecture: PIVOT’s Role in E²M² (Andres)
5:00-6:30pm: Mentor research presentations (Jean-Marius, Ornella, Antso)
6:30-7:30pm: Dinner

Thurs, Jan 18: “Refining Your Work”

6:30-8:00am: Breakfast
7:00-8:00am: Mentoring as needed
8:00-8:15am: Road Map and Daily Agenda (Amy)
8:15-10:00am: Lecture/Tutorial: Introduction to Network Modeling (Fidy)
10:00-10:30am: Break
10:30-12:00pm: Lecture/Tutorial: Introduction to Model Evaluation and Comparison (Jess)
12:00pm-1:00pm: Lunch
1:00-1:15pm: Final research plans (HW) (Cara)
1:15pm-3:00pm: Lecture/Tutorial: Introduction to Spatial Modeling (Amy)
3:00-4:00pm: Lecture: Modeling Extensions – Spatial mechanistic models (Tanjona)
4:00-4:30pm: Break
4:30-6:30pm: Work time + one-on-one mentoring sessions (all)
6:30-7:30pm: Dinner
7:30-9:30pm: Night hike: Ranomafana National Park (optional)

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

6:30-8:00am: Breakfast
7:00-8:00am: Mentoring as needed
8:00-8:15am: Road Map and Daily Agenda (Cara)
8:15-9:30am: Research Snapshots (all)
9:30am-10:30am: Discussion of a scientific paper (Tanjona + Mentors: Jean-Marius, Ornella, Antso)
10:30-11:00am: Break
11:00-11:50pm: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
11:50-12:00pm: Group photo
12:00-1:00pm: Lunch
1:00-2:00pm: Lecture: Looking back: How far have we come? (Tanjona)
2:00-3:00pm: Research plan work time + mentoring as needed (all)
3:00-5:00pm: Research plan work time on your own
5:00pm: Bus leaves CVB to take students to Ranomafana town (afternoon off)
7:30pm: Meet for dinner at Hotel Manja in Ranomafana town
9:30pm: Return bus to CVB

Sat, Jan 20: (Travel)

Mon, Jan 22: “Sharing Your Work” (at Institut Pasteur de Madagascar in Antananarivo)