2019 Syllabus

E2M2class

Please follow instructions for installing packages in R here.

Find your ‘Challenge and Mentoring’ Teams for the week here.

Saturday, Jan 12: ‘R Bootcamp’ (attendance optional) (at Institut Pasteur de Madagascar in Antananarivo)

8:00-8:30am: Brief Introductions (Cara)
8:30-10:00am: Intro to R Studio (Fidy)
- Knowing your working environment
- Assigning variables
- Basic arithmetic
- Running a script
10:00-10:30am: Coffee Break
10:30am-12:00pm: Small Groups: Software installation and catch-up. Mentors + instructors make sure all students have the proper materials installed and work through 4 tutorials with them. (Mentors)
12:00-1:00pm: Lunch
1:00-3:00pm: Lecture/Tutorial: Exploring & visualizing data in R (Christian)
3:00-3:30pm: Coffee Break
3:30-4:30pm: Lecture/Tutorial: Writing For-loops, If-Else Statements, and Functions in R (Cara)
4:30-5:30pm: Open mentoring session for outstanding questions

Sunday, Jan 13: “Travel Day”

6:00am: Meet at Institut Pasteur for departure to Ranomafana (lunch stop Antsirabe)
6:30-7:30pm: Dinner
7:30-8:30pm: Introductions (Cara) and Ice Breakers with data (Ben)

Monday, Jan 14 “Dealing with Data”

6:30-8:00am: Breakfast
8:00-8:30am: Road Map and Daily Agenda (Cara)
8:30-10:00am: Lecture: What are We Doing Here? Data and Models (Cara)
10:00-10:30am: Coffee Break
10:30-11:45am: Introductions: 2-min student/mentor/instructor introductions and mentor research presentations (Amy)
11:45am-12:00pm: Preparation for Women’s March Madagascar (Liz)
- Click here for discussion points about the Women’s March!
12:00-1:00pm: Lunch
1:00-2:00pm: Lecture: Linear regression and simple statistics (Andres)
2:00-3:00pm: Tutorial: Basic statistical modeling in R (Andres)
3:00-3:30pm: Coffee Break
3:30-5:00pm: Writing Exercise: Formulating Research Questions (HW) (Cara)
5:00-5:30pm: Beginning Malagasy Lesson (Mentors)
5:30-6:30pm: Free time, or one-on-one mentoring
6:30-7:30pm: Dinner

Tuesday, Jan 15: “Deeper Thinking With Data”

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; prep for hike
10:30am-1pm: Morning hike in Ranomafana National Park
1:00-1:45pm: Lunch
1:45-3:00pm: Exercise + Discussion: Dynamical Fever (Mentors + Christian)
3:00-4:00pm: Lecture: Study Design and Data Collection/Management (Amy/Ben)
4:00-4:30pm: Coffee Break
4:30-5:30pm: Group exercise: Refining research questions for modeling (HW) (Cara)
5:30-6:30pm: Free time, or one-on-one mentoring, or additional time for Tutorial: Mixed Modeling in R
6:30-7:30pm: Dinner

Wednesday, Jan 16: “Thinking About Mechanism”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda (Cara)
8:15-10:30am: Lecture/Tutorial: Introduction to Compartmental Models and Differential Equations (Amy)
10:30-11:00am: Coffee Break
11:00am-11:30pm: Writing Exercise: Creating a model world to address a research question (HW for tomorrow) (Cara)
11:30am-12:00pm: Small Group Session: Refining research questions for modeling (all instructors lead small groups)
12:00-1:00pm: Lunch
1:00-2:00pm: Small Group Session: Refining research questions for modeling (cont.) (all instructors lead small groups)
2:00-3:00pm: Small Group Discussion: Reading Keeling and Gilligan (Mentors + Sarah)
3:00-3:30pm: Coffee Break
3:30-4:45pm: Lecture w/Tutorial: Introduction to Occupancy Modeling (Fidy)
4:45-5:00pm: Additional Preparation for the Women’s March Madagascar (Liz)
4:45-5:45pm: Mid-session feedback. After the mentor-led feedback session, please fill out the online survey linked here. (Mentors)
6:00-6:40pm: Free time, or one-on-one mentoring
6:30-7:30pm: Dinner

Thursday, Jan 17: “Fitting Models to Data”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda (Cara)
8:15-8:30am: Response to Feedback (Ben)
8:15-9:45am: Lecture w/Tutorial: Model Fitting in Practice – the Basic Concept (Sarah)
9:45-10:15am: Coffee Break
10:15-11:15am: Lecture/Tutorial: Introduction to Spatial Modeling (Ben)
11:15-12:00pm: Exercise: Epidemics Cards (Cara + Sarah)
12:00-1:00pm: Lunch
1:00-2:00pm: Tutorial: Model Fitting with Epidemic Cards (Cara)
2:00-3:30pm: Model Telephone with Model Diagrams (Mentors + Christian)
3:30-4:00pm: Coffee Break
4:15-4:30pm: Final research plans (HW) (Cara)
4:30-6:00pm: Work time + student-instructor meetings
6:00-6:30pm: Complete “Challenge Group” Activities (Ben)
6:30-7:30pm: Dinner
8:00pm: Night walk Ranomafana National Park (optional)

Friday, Jan 18: “Refining Your Work”

6:30-8:00am: Breakfast
8:00-8:30am: Road Map and Daily Agenda (Cara)
8:30-10:00am: Teaching/Tutorial: Model Selection and Comparison (Cara)
- We will not be teaching this tutorial, but feel free to work through ‘Model Comparison with Age Prevalence Data’ on your own time.
10:00-10:30am: Coffee Break
10:30-12:00pm: Lecture w/Tutorial: Introduction to Network Modeling (Fidy)
12:00pm-1:00pm: Lunch
1:00-1:30pm: Group photo - Wear your E2M2 shirts!
1:30-3:00pm: Lecture/Tutorial: Modeling Vector-Borne Disease (Amy/Ben)
3:00-3:30pm: Coffee Break
3:30-4:15pm: Research Snapshots (instructors)
4:15-5:15pm: Mentor research presentations (10 min each) (Mentors)
5:30-6:30pm: Work time + one-on-one student-instructor meetings (all)
6:30-7:30pm: Dinner

Saturday, Jan 19: “Putting It All In Perspective”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda (Cara)
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
10:00-11:00am: Lecture: Looking back: How far have we come? (Fidy)
11:00am-12:00pm: Work time + one-on-one student-instructor meetings (all)
12:00-1:00pm: Lunch
1:00-6:30pm: Women’s March Madagascar (optional), March will proceed from CVB to Ranomafana town. Speakers and activities for all who are interested. (Liz)
6:30-9:00pm: Farewell dinner in Ranomafana town (Hotel Manja)
9:30pm: Return bus to CVB

Sunday, Jan 20: (Travel Day)

5:00-6:00am: Breakfast to go
6:00am: Board bus
Return to Antananarivo
Please upload your final slide presentations here by midnight on Sunday, January 20, 2019!

Monday, January 21: “Sharing Your Work” (at Institut Pasteur de Madagascar in Antananarivo)

9:00-11:00am: Closing ceremony and final student presentations (Cara)
11:00am-12:00pm: Final Feedback Session (Julio + Mentors)
12:30-2:00pm: Farewell lunch
2:00-4:30pm: Mini-symposium: “Modeling Insights Into Epidemiology and Ecology” (Instructor presentations)
- Instructor and mentor research presentations, (TBA, 5-10 min each + questions)
4:30pm: Social Hour