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)

8:00-9:00am: Lecture: Writing For-loops, If-Else Statements, and Functions in R (Fidy)
9:00-10:00am: Tutorial: Writing For-loops, If-Else Statements, and Functions in R (Fidy, with help from mentors)
10:00-10:30am: Coffee Break
10:30-11:30am: Lecture: Data Cleaning in R (Christian)
11:30am-12:30pm: Tutorial: Data cleaning in R (Christian, with help from Mentors)
12:30-1:30pm: Lunch
1:30-2:30pm: Lecture/Tutorial: Intro to Spatial Visualization and Plotting (Fidy)
2:30-3:30pm: Time for students to load and clean their own datasets if they have them. Otherwise, students are free to go home.
3:30-4:00pm: Coffee Break
4:00-5:00pm: Open mentoring session for outstanding questions or continued work on tutorials from above

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”

6:30-8:00am: Breakfast
8:00-8:30am: Road Map and Daily Agenda. Brief Introductions (Cara)
8:30-9:00am: Lecture: What are We Doing Here? Ecology Meets Epidemiology (Cara)
9:00 - 10:00am: Lecture: Data and Models (Tanjona)
10:00-10:30am: Coffee Break
10:30-12:00pm: Lecture: Reviewing Key Concepts in Mathematics (Tanjona)
12:00-1:00pm: Lunch
1:00-2:00pm: Introductions: 2-min student introductions (Sarah)
2:00-3:30pm: Formulating research questions (Cara)
- For HW, write your own research question
3:30-4:00pm: Coffee Break
4:00-6:00pm: Lecture/Tutorial: Study Design and Data Collection (Sarah)
6:30-7:30pm: Dinner

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)
- Assigned groups are posted here.
- All students should have a workable statistical and mechanistic question by the end of the session
- For HW, assign: Creating a Model world + a Statistical Framework
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”

6:30-8:00am: Breakfast
8:00-8:15am: Road Map, Daily Agenda, and Response to Feedback (Cara)
8:15-9:30am: Lecture w/Tutorial: Model Fitting in Practice – the Basic Concept (Sarah)
9:30-10:30am: Lecture/Tutorial: Introduction to Network Modeling (Andres)
10:30-11:00am: Coffee Break
11:00am-12:00pm: Exercise: Epidemic Cards (Christian, Cara, and Mentors)
12:00-1:00pm: Lunch
1:00-2:00pm: CVB tour with Patricia Wright
2:00-3:00pm: Tutorial: Model Fitting with Epidemic Cards (Cara)
3:00-3:30pm: Coffee Break
3:30-4:30pm:Small Group Discussion: Reading a Research Paper (Fara, Sarah, Mentors)
4:45-6:30pm: Work time + One-on-One Student-Instructor meetings (All Instructors)
6:30-7:30pm: Dinner
8:00pm: Night walk Ranomafana National Park (optional) (Mentors)

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

6:30-8:00am: Breakfast
8:00-8:15am: Road Map and Daily Agenda
- Please make edits to this google doc by midnight on Sunday, January 12 if you would like to change how your name is written on your final certificate!
8:15-8:45am: Final research plans (HW) and Research Snapshots (Cara, Sarah, Fara, Andres)
8:45-10:00am: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
10:00-10:30am: Coffee Break
10:30-11:15am: Lecture/Tutorial: Model Selection and Comparison (Cara)
11:15am-12:00pm: Lecture: Looking back: How far have we come? (Tanjona)
12:00-1:00pm: Lunch
1:00-1:30pm: Group photo - Wear your E²M² shirts!
1:30-2:30pm: Work time + One-on-One Student-Instructor Meetings (optional) (All Instructors)
- Sign up here if desired to meet with an instructor one last time.
2:30-3:30pm: Instructors and mentors meet. Assignments here.
6:30-9:00pm: Farewell dinner in Ranomafana town (Hotel Manja)
9:30pm: Return bus to CVB

Sunday, Jan 12: (Travel Day)

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)
- Instructor and Mentor Research Presentations
4:30pm: Social Hour