Chapter 5: From Animations to Science

March 31, 2023

Learning Objectives

  • Learn the importance of version control.
  • Understand the concept that using ABMs for science means:
    1. measuring system response and behavior through producing quantitative output, and
    2. conduct simulation experiments (in silico).
  • Perform your first simulation experiment.
  • Define and initialize a global variable by creating a slider or switch.
  • Develop an understanding of what reporters are and how to write them.

Learning Objectives

  • Start learning how to find and fix mistakes in your code.
  • Learn to create output by:
    1. writing text to an output window,
    2. creating a time-series plot, and
    3. exporting plot results to a file.
  • Create a version of the Butterfly model that uses real topographic data by importing data into NetLogo.

Programming Note

Moving global variables to the Interface

  • GUI (Graphical User Interface) elements on the Interface both define and initialize a global variable. What this means if you move a variable to the Interface:
  • You should comment out the variable in the globals [ ] chunk of code. I would also put an additional comment at the end stating it is on the Interface. For example: <br >
globals
[
  ; q  ; (Interface Slider) Probability that ...
]

Programming Note

Moving global variables to the Interface

  • GUI (Graphical User Interface) elements on the Interface both define and initialize a global variable. What this means if you move a variable to the Interface:
  • You should remove or comment out the variable initialization in the setup procedure. If you choose to comment and not remove, I would also put the same comment from the globals chunk in here as well. For example:
to setup
[
  ; set q 0.2  ; (Interface Slider)
]

Programming Note

Initializing variables

  • New variables have a default value of zero until assigned another value.
  • Good practice is to explicitly set it to zero anyways in the code.

Programming Note

Troubleshooting tips

Tips to reduce probability of getting stuck and increase probability of getting unstuck.

  • Proceed slowly! Add small chunks of code at a time, check for syntax (using Check button) and runtime (using Go button) errors, and verify and validate code (i.e. is it doing what it is supposed to do?) For verification and validation:
    1. Create a Step button that steps through the program one tick at a time.
    2. Use show statements throughout your code.
    3. Use Agent Monitors.

Programming Note

Troubleshooting tips

Tips to reduce probability of getting stuck and increase probability of getting unstuck.

  • Think logically!
    1. “It should work this way because…,” i.e. critically assess output and results and see if they make sense
    2. “Let me try this and see what happens…”

Intro to Quantitative Biology, Spring 2023