Assignments on EES 4760/5760

Set up NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

There is nothing for you to turn in, but do the following task to prepare for next week:

Homework Exercises:

Download NetLogo version 6.4.0 from https://ccl.northwestern.edu/netlogo/ and install it on your computer.

Introducing NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

As you read along with Section 2.3, follow along on your computer and build the Mushroom Hunt model by typing in the code shown in the textbook. The whole program is shown on pages 27–29. Save your model as mushroom_hunt.nlogo.

This exercise may seem very simple, but it is the first step toward learning how to program NetLogo and it will be an important first step toward writing your own models.

Becoming familiar with NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

This homework consists of reading and working through tutorials, so there is nothing to turn in.

Homework Exercises:

Everyone should do exercises 2.1 and 2.2 in Chapter 2 of Railsback & Grimm. This consists of reading and working through tutorials, so there is nothing to turn in.

Experimenting with NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

Upload your work to Brightspace when you’re done (Word or text files for the descriptions and ODD document, and .nlogo files for your NetLogo models).

When there is more than one file for a homework assignment, I recommend that you make a Zip file containing all of the files for the different parts of the assignment and upload the Zip file to Brighspace instead of uploading the files separately. When a homework assignment has more than one problem, and each problem has multiple files, it can be helpful to have a separate folder for each problem, and put all of these folders into the ZIP file that you turn in.

Science with models: Butterfly mating

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

Some problems in this homework set call for you to write a NetLogo model and also answer questions about the model. For answering the questions, you may take any of these approaches:

Edit the INFO page for your NetLogo model and add the following (this example is for exercise 5.4)
```
# Exercise 5.4

When I ran the model ...
```
Write your answer in a Word file or other document file (text, PDF, etc.) with the title homework_answers.docx and put the homework answers in there, as follows:

Reproducing a model from its ODD

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Graduate Students:
- Graduate students should do Railsback & Grimm, Ex. 5.11

Notes on Homework:

Graduate Students: You can download the journal article for this exercise, R. Jovani & V. Grimm. (2008) “Breeding synchrony in colonial birds: From local stress to global harmony”, Proc. Royal Soc. London B 275, 1567–63 from the class web site, https://ees4760.jmgilligan.org/files/models/chapter_05/Jovani_Grimm_2008_Breeding.pdf.

You don’t have to reproduce all of the figures in the paper. Focus on reproducing the information in Figure 2 (make a figure of colony synchrony versus NR and some other figures showing histograms of breeding dates for NR = 0.00, 0.08, 0.20, and 1.00 and comparing them to the histograms in Fig. 2.

Research project proposal

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a one-to-two page (double-spaced) proposal for your semester research project.

Notes on Homework:

This proposal should describe the topic you want to work on, identify a published open-source model you want to work with, and and describe how you think you might want to extend it.

You should consult the textbook, the Model Library in NetLogo, and the list of reading and computational tools and resources I distributed on the first day of class (it’s also posted on the course web site).

Testing and debugging

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Everyone:
- Railsback & Grimm, Ch. 6, Ex. 6.2, 6.3
Graduate Students, also do the following:
- Railsback & Grimm, Ch. 6, Ex. 6.4, 6.5

Notes on Homework:

You do not need to turn anything in for Exercise 6.2. This is an exercise to try for the experience

A hint for exercise 6.3: Patches have integer coordinates (representing the center of the patch). How does the turtle determine the angle to face during setup? How does it determine the angle to face in go-back? Can you think of a different way to record the path so the go-back exactly retraces the path it took during setup? If you knew the direction the turtle was heading at each step during setup, could you use this heading information to exactly retrace the path?

Analyzing model experiments

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Everyone:
- Railsback & Grimm, Ch. 8, Ex. 8.1, 8.2
- Railsback & Grimm, Ch. 9, Ex. 9.3, 9.4
Graduate Students, also do the following:
- Railsback & Grimm, Ch. 8, Ex. 8.3, 8.4
- Railsback & Grimm, Ch. 9, Ex. 9.6

Programming agent sensing

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Optional: The following exercises are optional. You can turn them in for extra credit.

Railsback & Grimm, Ch. 10, Ex. 10.1
Railsback & Grimm, Ch. 11, Ex. 11.1

Team modeling project presentations

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Teams will give a presentation on their projects.

Notes on Homework:

See the team project assignment sheet for details on what I expect for the presentation.

Research project model analysis

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Study the code and ODD of the model you chose for your semester research project, play with the model and run some BehaviorSpace experiments to examine its output.

Turn in a 3–5 page (double-spaced) write-up about the model.

Notes on Homework:

See the project assignment sheet for details about this assignment.

Team modeling project report

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in the written report for your team project on Brightspace.

Notes on Homework:

See the team project assignment sheet for details.

Research project ODD

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in an ODD for extending your chosen model to ask new questions.

Notes on Homework:

See the semester research project assignment sheet for details.

Draft model code for research project

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a draft .nlogo file with your modified model. The ODD for your modified model should be included in the “Info” section of the model.

You should also turn in a document that describes what you are satisfied with about your draft model and what problems you are struggling with.

Notes on Homework:

The model code you turn in should run, but it does not need to be perfect.

Research project presentation

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

You will make a five-minute presentation in class about your model (You can use the full five minutes of talking and there will be an additional two minutes for questions).

Notes on Homework:

There will not be time to go into all the details in your presentation, so focus on:

Structure:

Start by describing your research question
Briefly describe your model
Describe the experiments you performed:
- What outputs did you observe or measure?
- What parameters did you change?
- What did you see? (e.g., behaviorspace graphs or screenshots of the model)
Conclusions

General recommendations:

5 slides, one minute each.
As much as you can, use figures (graphs, illustrations, images, etc.) instead of text.
Avoid slides with a lot of text

You can’t say everything you did, so focus on the most interesting highlights.

Research project presentation

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

You will make a five-minute presentation in class about your model (You can use the full five minutes of talking and there will be an additional two minutes for questions).

Notes on Homework:

There will not be time to go into all the details in your presentation, so focus on:

Structure:

Start by describing your research question
Briefly describe your model
Describe the experiments you performed:
- What outputs did you observe or measure?
- What parameters did you change?
- What did you see? (e.g., behaviorspace graphs or screenshots of the model)
Conclusions

General recommendations:

5 slides, one minute each.
As much as you can, use figures (graphs, illustrations, images, etc.) instead of text.
Avoid slides with a lot of text

You can’t say everything you did, so focus on the most interesting highlights.

Research project report

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a written report about your research project. Your report should follow the model of a research report for Science magazine:

Notes on Homework:

Your report should have the following structure:

Abstract (1 paragraph summary of the paper, focusing on highlights)
Introduction
- Research question and why it’s interesting
Methods
- Describe the model you started with and how you changed it to answer your research question
- Describe the experiments you ran with the model.
- Describe what outputs you measured
Results
- What did you see (graphs of output, pictures of turtles on patches, etc.)
Discussion, conclusions:
- What did you learn from the results of your experiment?
- If you had more time, what would you do next with your model?
- Do you think these results point to possible uses for your model?
References

See the assignment for further details.