2024 Syllabus

Please follow instructions for installing packages in R here.

Please download this folder of sequences to your personal computer prior to departing Antananarivo.

DATE TO BE DETERMINED: Intro to R Bootcamp

  • R-Bootcamp is a one-day optional session held at Madagascar Biodiversity Center in Tsimbazaza, Antananarivo, which we offer as a resource for students who need to brush up on programming skills prior to the start of the formal course.

  • Please make sure to have all software installed and work through the Intro Tutorials prior to arriving to class

  • 8:00-8:15am: Brief Introductions
  • 8:15-9:15am: Lecture: Intro to R Studio
  • 9:25-10:00am: Tutorial: Intro to R Studio
  • Includes:
    • Knowing your working environment
    • Assigning variables
    • Basic arithmetic
    • Running a script
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture/Tutorial: Project organization in R
  • 12:00-1:30pm: Lunch + extra time if certain students need extra time for downloads/installations.
  • 1:30-2:30pm: Lecture: Exploring & visualizing data in R
  • 2:30-3:30pm : Tutorial: Exploring & visualizing data in R
  • 3:30-4:00pm: Coffee Break
  • 4:00-5:00pm: Lecture/Tutorial: Intro to for-loops, if-else statements, and functions

Saturday, Jan 6: “Travel Day”

  • 5:30am: Meet at Institut Pasteur for departure to Ranomafana (lunch stop Ambositra)
  • 6:30-7:30pm: Dinner

Sunday, Jan 7: “Data and Models”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Brief Introductions
  • 8:30-10:00am: Lecture: Data and Models
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Introductions: 2-min student introductions
  • 12:00-1:00pm: Lunch
  • 1:00-3:00pm: Formulating research questions
    • For HW, write your own research question
  • 3:00-3:30pm: Coffee Break
  • 3:30-5:00pm: Lecture/Tutorial: Intro to Basic Statistical Models
    • distributions, t-tests, chi-squared, ANOVA
  • 6:30-7:30pm: Dinner

Monday, Jan 8: “Two Broad Classes of Model”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda
  • 8:15-10:00: Lecture/Tutorial: Intro to Linear Regression
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture: Introduction to Compartmental Models
  • 12:00-1:00pm: Lunch
  • 1:00pm-2:00pm: Tutorial: Building Mechanistic Models in R
  • 2:00-3:00pm: Exercise + Discussion: Dynamical Fever
  • 3:00-3:30pm: Coffee Break
  • 3:30-4:00pm: Large Group Session: Refining research questions for modeling
    • Refine questions from yesterday and develop statistical frame work + model diagram
  • 3:30-5:30pm: Small Group Sessions: Refining research questions for modeling
    • All students should have a workable statistical and mechanistic question by the end of the session
    • For HW, ‘Creating a Model World + Building a Statistical Framework’, will be due on Wednesday, Jan 10
  • 6:30-7:30pm: Dinner

Tuesday, Jan 9: “More Complex Study Design”

  • 6:30-7:30am: Breakfast
  • 7:30am-12:00pm: Morning hike in Ranomafana National Park
    • Meet out front of CVB! Get your breakfast early
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Lecture/Tutorial: Model Guided Study Design
  • 2:00-3:00pm: Work time + One-on-One Student-Instructor Meetings
  • 3:00-3:30pm: Coffee Break
  • 3:30-5:00pm: Lecture/Tutorial: Introduction to Mixed Modeling
  • 5:00-6:00pm: Mid-Session Feedback
  • 6:30-7:30pm: Dinner

Wednesday, Jan 10: “Fitting Models to Data”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map, Daily Agenda, Response to Feedback
  • 8:30-10:00am: Lecture/Tutorial: Model Fitting in Practice – the Basic Concept
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Activity: Epidemic Cards
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Tutorial: Model Fitting with Epidemic Cards
  • 2:00-3:30pm: Activity: Model Telephone with Model Diagrams
  • 3:30-4:00pm: Coffee Break
  • 4:00-5:30pm: Small Group Discussion: Reading a Research Paper
  • 6:30-7:30pm: Dinner
  • 7:00pm: Night walk Ranomafana National Park (optional)
    • Meet out front of CVB!

Thursday, Jan 11: “Refining Your Work”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map, Daily Agenda
  • 8:15-10:00am: Lecture + Activity: So many models! How to choose?!?
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture/Tutorial: Model Selection and Comparison
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Lecture/Tutorial: Introduction to Phylogenetic Modeling
  • 2:30-3:00pm: Coffee Break
  • 3:00-4:00pm: Lecture/Tutorial: Introduction to Network Models
  • 4:00-4:15pm: Final research plans (HW)
  • 4:15-4:45pm: Research Snapshots
  • 4:45-6:00pm: Work time + One-on-One Student-Instructor Meetings
  • 6:30-7:30pm: Dinner

Friday, Jan 12: “Putting It All In Perspective”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda
  • 8:15-9:30am: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication
  • 9:30-10:00am: Coffee Break
  • 10:00am-11:45am: Student presentations
  • 11:45am-12:00pm: Group photo - Wear your E2M2 shirts!
  • 12:00-1:00pm: Lunch
  • 1:00-1:30pm: Lecture: Looking back: How far have we come?
  • 1:30-3:00pm: One-on-One Student-Instructor Meetings
  • 3:00-6:30pm: Work time + free time in town
  • 6:30-9:00pm: Farewell dinner in Ranomafana town
  • 9:30pm: Return bus to CVB

Saturday, Jan 13: (Travel Day)

  • 5:00-6:00am: Breakfast to go
  • 6:00am: Board bus
  • Return to Antananarivo

Sunday, Jan 14: Open Work Day at MBC

  • 9:00am-4:00pm: Madagascar Biodiversity Center will be open with internet and instructors available for students to get help and prepare for Monday’s Symposium.

Final Symposium on Monday, January 15, 2024 at Madagascar Biodiversity Center