2022 Syllabus (Tentative)

Please follow instructions for installing packages in R here.

Friday, Dec 9: Intro to R Bootcamp

  • R-Bootcamp is a one-day optional session held at Institut Pasteur de Madagascar in 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.

  • 8:00-8:30am: Brief Introductions (Fidy)
  • 8:30-9:30am: Lecture: Intro to R Studio (Fidy)
  • 9:30-10:00am: 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)
  • 10:00-10:30am: Coffee Break
  • 10:30am-11:30am: Tutorial: Intro to R Studio (Fidy, with help from Mentors)
    • Includes:
      • Knowing your working environment
      • Assigning variables
      • Basic arithmetic
      • Running a script
  • 11:30-1:00pm: Lunch + extra time if certain students need extra time for downloads/installations.
  • 1:00-2:00pm: Lecture: Exploring & visualizing data in R (Christian)
  • 2:00-3:00pm : Tutorial: Exploring & visualizing data in R (Christian, with help from Mentors)
  • 3:00-3:30pm: Coffee Break
  • 3:30-4:30pm: Lecture/tutorial: Intro to for-loops, if-else statements, and functions (Fidy)
  • 4:30-5:30pm: Open mentoring session for outstanding questions or continued work on tutorials from above or from homework (All instructors + mentors)

Saturday, Dec 10: “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

Sunday, Dec 11: Getting Started with the Basics

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Brief Introductions
  • 8:30-10:00am: Lecture: Models and Data (Cara)
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Introductions: 2-min student introductions
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Formulating research questions (Cara)
    • For HW, write your own research question
  • 2:30-3:00pm: Coffee Break
  • 3:00-5:00pm: Lecture/Tutorial: Overview of Basic Statistical Concepts in R (Sophia?)
  • 6:30-7:30pm: Dinner

Monday, Dec 12: “Using Models with Data”

  • 6:30-8:00am: Breakfast
  • 8:00-8:30am: Road Map and Daily Agenda
  • 8:30-10:00am: Lecture/Tutorial: Model Guided Study Design (Cara)
    • Please read ‘Model-Guided Field Work’ by Restif et al. 2012. prior to coming to class
    • Lesson will idea of power analysis for statistical design and/or simulation for mechanistic design
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture/Tutorial: Linear Regression and Simple Statistics (Andres)
  • 12:00-1:00pm: Lunch
  • 1:00-2:30pm: Lecture: Introduction to Compartmental Models (Sophia)
    • Lecture should introduce terms and review concepts of stochastic/deterministic model and discrete/continuous time
  • 2:30-3:00pm: Coffee Break
  • 3:00-3:30pm: Large Group Session: Refining research questions for modeling (All Instructors)
    • Refine questions from yesterday and develop statistical frame work + model diagram
  • 3:30-5:30pm: Small Group Sessions: Refining research questions for modeling (All instructors lead small groups)
    • All students should have a workable statistical and mechanistic question by the end of the session
    • For HW, assign: ‘Creating a Model World + Building a Statistical Framework’ (but it will not be due until Wednesday)
  • 6:30-7:30pm: Dinner

Tuesday, Dec 13: “Applying Simple Models”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda
  • 8:15-9:30am: Tutorial: Building Mechanistic Models in R (+ Review from Monday Compartmental Models Lecture) (Sophia)
  • 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: Exercise + Discussion: Dynamical Fever (Gwen + Sophia)
  • 2:30-3:30pm: Lecture/Tutorial: Introduction to Mixed Modeling (Andres)
  • 3:30-4:00pm: Coffee Break
  • 4:00-5:30pm: Work time + One-on-One Student-Instructor Meetings (All Instructors)
    • Students should fully develop their Statistical Frameworks and Model Diagrams today
  • 5:30-6:30pm: Mid-Session Feedback
  • 5:30-6:30pm: Mentors practice presentations with instructors. Students do not need to attend.
  • 6:30-7:30pm: Dinner

Wednesday, Dec 14: “Refining Your Work”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda, and Response to Feedback
  • 8:15-10:00am: Lecture w/Tutorial: Model Fitting in Practice – the Basic Concept (Gwen)
  • 10:00-10:30am: Coffee Break
  • 11:30am-12:00pm: Lecture/Tutorial: Model Selection and Comparison (Gwen + Cara)
  • 12:00-1:00pm: Lunch
  • 1:00-1:45pm: Exercise: Epidemic Cards (Gwen + Sophia)
  • 1:45-2:30pm: Tutorial: Model Fitting with Epidemic Cards (Gwen + Sophia)
    • Add some model comparison via AIC to tutorial
  • 2:30-3:00pm: Coffee Break
  • 3:00-4:00pm: Small Group Discussion: Reading a Research Paper (Christian + Cara)
  • 4:00-5:00pm: Model Telephone with Model Diagrams (Cara)
  • 5:00-6:30pm: One-on-One Student-Instructor Meetings (All Instructors)
  • 6:30-7:30pm: Dinner
  • 8:00pm: Night walk Ranomafana National Park (optional)

Thursday, Dec 15: “Bells and Whistles”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map, Daily Agenda
  • 8:15-9:15am: Lecture/Tutorial: Introduction to Network Modeling (TBA)
  • 9:15-10:00am: Lecture/Tutorial: Introduction to Occupancy Modeling (TBA)
    • May replace with ‘Community Biodiversity Analyses’ or ‘GAMs’ or slot in ‘Phylogenetics’ or just have one lecture in this slot
  • 10:00-10:30am: Coffee Break
  • 10:30am-12:00pm: Lecture/Tutorial: Introduction to Spatial Visualization and Plotting (Sophia?)
  • 12:00-1:00pm: Lunch
  • 1:00-2:00pm: Activity: The Metapopulation Game (Cara)
  • 2:00-3:00pm: Lecture/Tutorial: Modeling Insights from the Metapopulation Game (Cara)
    • Would be great to make a tutorial that shows how to build this model and uses data from this game.
  • 3:00-3:30pm: Coffee Break
  • 3:30-4:00pm: Final research plans (HW) (Cara)
  • 4:00-4:30pm: Research Snapshots (All Instructors)
  • 4:30-6:30pm: Work time + One-on-One student-instructor meetings
  • 6:30-7:30pm: Dinner

Friday, Dec 16: “Putting It All In Perspective”

  • 6:30-8:00am: Breakfast
  • 8:00-8:15am: Road Map and Daily Agenda
  • 8:15-9:15am:Lecture/Tutorial: Introduction to Phylogenetic Modeling (Gwen)
  • 9:15-10:30am: Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication (Andres)
  • 10:30-11:00am: Coffee Break
  • 11:00-11:30am: Lecture: Looking back: How far have we come? (Cara)
  • 11:30am-12:00pm: Group photo - Wear your E2M2 shirts!
  • 12:00-1:00pm: Lunch
  • 1:00-6:30pm: Work time + one-on-one student-instructor meetings (All Instructors)
  • 6:30-9:00pm: Farewell dinner in Ranomafana town (Hotel Manja)
  • 9:30pm: Return bus to CVB

Saturday, Dec 17: (Travel Day)

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

TBA: Final Symposium in January 2023

  • Students will have the opportunity to present their work in a final symposium in January 2023 at Institut Pasteur de Madagascar in Antananarivo. Participation in this symposium will not be optional, based on students’ availability and is not required for application to the course. Details about the date and schedule for this synposium will become available prior to the course start date.