Week 15

Quiz on Tuesday 4/30

The quiz will be on one or more of the following items.

• Problems # 1 and 2 p. 94; # 3, 4, and 5 p. 95.
• Problems # 1 and 2 p. 116, # 3 and 5 p. 117, # 12 p. 118.

Poster Session on Thursday 5/2

• The poster session will be held from 10 to 11:15 am in the ENR 2 Courtyard. Campus map: http://map.arizona.edu/.
• Plan to arrive between 9:30 am and 9:45 am to allow time to sign in and set up your poster.

Due on Monday 5/6

• Final report.
• Written end-of-semester reflection.
• Please see detailed assignments on D2L. Also note that both D2L folders close at 6:15 pm on 5/6.

Please remember to fill out the online TCEs

• Any feedback you may have on the course content and in-class activities, as well as online notes and assignments will be greatly appreciated.
• Thank you!

Week 14

Quiz on Thursday 4/25

The quiz will be on one or more of the following items.

• Problems # 1, 2 and 4 p. 84, # 5 p. 85.

Poster due on Thursday 4/25

• Please submit PDF and PPTX versions of your poster.
• The PowerPoint template is set up to have a print size of 36 by 24 inches when saved as a PDF. If you use Google Slides to edit your poster, please make sure that when you export the document in PowerPoint format, the print size has not changed.
• To check the size, save the PowerPoint file as a PDF. Do not use the "Print as PDF" option since this would add blank spaces around the poster to match the letter-size aspect ratio. Then look at the properties of your PDF file. In the Description tab, under Advanced, it should say: Page Size: 36.00 x 24.00 in. If it doesn't, please fix the problem before uploading your poster to the submission folder.
• Groups must have registered their posters and submitted their posters for printing by 8 am on 4/26. Please see detailed instructions on D2L.

Week 13

Population Dynamics Lab due on 4/18

Please see instructions at https://sites.google.com/math.arizona.edu/math-485-spring-2019/population-dynamics-lab.

Your work should consist in a typed report (in PDF format) and either a set of codes or an Excel (or similar) spreadsheet with your calculations. Place these documents in the D2L Assignment Submission Folder called Population Dynamics Lab.

Week 12

Quiz on Tuesday 4/9

The quiz will be on one or more of the following items.

• Problem # 5 page 70.
• Problems # 11 through 14 page 71.

Week 11

Quiz on Tuesday 4/2

The quiz will be on one or more of the following items.

• Problems # 4 through 10, pages 33-34.
• Problems # 1 & 4 pages 69-70.

Weeks 9 & 10

Thursday 3/21 & Tuesday 3/26

Midterm presentations. Each group should prepare a 15-minute presentation describing the team, its project, and the results so far. Guidelines are below.

• Amend the slides you used for your initial presentation: keep slides 1-4 (see previous assignment) and replace Slide 5 by a description of your results so far. Make sure to take into account the feedback you received after your first presentation: fix any typos, issues, references, etc. Add slides discussing your results and describing what remains to be done.
• Use as many slides as needed, keeping in mind that pictures and/or videos are useful visual aids, and that your presentation should not exceed 15 minutes. There will be time for questions at the end.
• If you have developed codes that run reasonably quickly, consider demonstrating how they work during your presentation.
• Also take into account my comments on your midterm report: be prepared to address any questions I raised, make sure to fix any typos or calculation errors, etc. It should be clear from your presentation that you have understood my comments and have thought about how to address them.
• Each team member should contribute to the presentation in a significant way and be able to answer questions.

Place a PDF copy of your slides in the D2L folder called Midterm Presentation.

Week 8

Due Thursday 3/14

Download and read the PDF version of R. May's article entitled Simple mathematical models with very complicated dynamics. As usual, you will need to use your UA credentials to access the file. Then answer questions (1), (3), (5), (6), (7), (12), (13), and (14) of Problem # 15 on page 72 of the class notes, plus two questions of your choice, chosen among the remaining questions.

Please place your homework, in the form of a single file in PDF format, in the D2L Assignment Submission Folder called Homework 2.

Week 7

Quiz on Tuesday 2/26

The quiz will be on one or more of the following items.

• Problems # 11 & 12 p. 35, # 15 p. 36, # 18, 19, 20 and 21 p. 37, # 22 and 23 p. 38.
• For Problems 11, and 19-22, check your answers with PPLANE.

Midterm Reports due on Thursday 2/28

Place a single file in PDF format in the folder called Midterm Report. Please submit only one report per group and note that the folder closes at 2 pm on 2/28.

Week 6

Start Drafting your Report

• Midterm project reports are due before Spring Break.
• Do not paraphrase, make sure to include appropriate references, and credit your sources. If you reproduce figures or tables from articles you read, explain how they were reproduced/obtained, and cite the original articles in the captions.

Recommended Report Components

1. Abstract: in a few sentences, describe what your project is about, what type of model you are using, what results you have obtained, as well as their significance.
2. Introduction: describe the problem that is being addressed as well as its significance/importance. Use information from the context articles provided as well as from your literature searches.
3. Methods: describe any data collection process, as well as the model(s) you are using. Clearly explain what assumptions are being made and how each model works. For agent-based models, make sure to describe how each agent is expected to behave in each situation it may encounter.
4. Results: for a midterm report, these will probably be preliminary. Show that the components (codes, model equations) already developed as part of the modeling process work as they should. If appropriate, perform a dimensional analysis of your model and identify relevant scales or dimensionless combinations of parameters.
5. Discussion: summarize what you have accomplished so far as part of the project and discuss your results: what works as expected, what needs to be addressed, what remains to be done.
6. Conclusion: summarize the contents of your report and consider possible extensions of your work.

Required Report Components

At the end of your report, detail the contribution of each team member. There should be two statements.

• A statement indicating which team member takes responsibility for specific parts of the report. For instance: "X wrote the codes for <specify part of the project>; Y performed the analysis of Section <section number>; Z collected the data from online sources. All team members read and approved the entire report."
• A statement indicating the amount of effort each team member put into the project. This should read as follows: either "All team members contributed equally to this project" or "X is responsible for x% of the project; Y is responsible for y%; ..." This statement will affect the numerical score of each team member.

Week 5

Quiz on Thursday 2/14

The quiz will be on one or more of the following items.

• Agent-based models.
• Problems # 1 & 3 p. 32, # 4 & 5 p. 33, # 8 & 9 p. 34, # 12 & 13 p. 35, # 14, 15, & 16 p. 36.

Reading assignment

Section 12.4 of the notes (starting on page 133) on eigenvalues and eigenvectors, and Section 14.6 (starting on page 158) on phase plane analysis.

Week 4

By Tuesday 2/05

Read the article by Eric Bonabeau entilted Agent-based modeling: Methods and techniques for simulating human systems.

Week 3

Due Tuesday 1/29

In-class initial presentations. Prepare a 5-minute presentation describing your group and your project. You should cover all of the topics mentioned in the following template.

• Cover slide: title of your project, your names, your mentor's name.
• First slide: description of your team, who is doing what (remember roles and responsibilities may change throughout the semester). Indicate when your team meets, both on its own and with its mentor. Make sure each there is at least one team member in charge of each goal and learning objective.
• Second slide: what the project is about (include contextual information as well as specifics), the articles you are using (include full references).
• Third slide: describe the type of model used in the article(s), the hypotheses, and the type of approach used to explore the model (analysis, numerical solution, etc).
• Fourth slide: describe the results presented in the article(s).
• Fifth slide: indicate what you plan to do for your project. In particular, describe your plans for working through the derivation of the model and testing it, list the results you would like to reproduce, as well as any extensions of the model you intend to explore.

Place a copy of your slides in PDF format in the D2L folder called Initial Presentation. The folder will close at 2 pm on 1/29.

Quiz on Thursday 1/31

The quiz will be on one or more of the following problems.

• Problems # 1, 2, 3, 4, and 6 p. 15 (this refers to the course notes in PDF format available in D2L - look for Textbook in the course contents; if you use the newer, online version of the notes, the problems are at the end of chapter 2 and the numbers are the same). Links to the articles mentioned in Problem # 6 are below. As usual, you will need to use your UA credentials to access the full text of these articles.
• Mexican waves in an excitable medium
• Human waves in stadiums

Week 2

By Thursday 1/24

You should have done the following:

• Met with your mentor as a group.
• Identified a time of the week when your group will meet with your mentor during the semester, and when your group will meet on its own - online meetings are acceptable if needed.
• Assigned roles within your group. There are two categories of roles, and both types should be considered.

1. Group organization. Examples of tasks include taking notes during meetings and sending a summary to the group; coordinating input from each group member; submitting reports and presentations to D2L on behalf of the group; proofreading presentations slides, the poster, or the final report. These roles can change or evolve throughout the semester but at the end of each meeting, it is important that everyone knows what they need to have accomplished before the next group meeting.
2. Project development. It is highly recommended that each group member be responsible for at least one of the learning objectives or project goals listed in the description of each project. Specific activities related to these assignments include searching the literature and writing up findings; coding up a numerical simulation; working through the derivation of some equations and sharing your understanding with the group; creating figures and tables to summarize parameters or results; drafting your assigned section of the next report or presentation.

Week 1

By Monday 1/14

Fill out the Project Preferences survey in D2L.

Install MATLAB on your laptop and bring it to class. If you prefer to program in Python, R, or C, this is fine as well.

Due Thursday 1/17

Read the chapter on the nature of mathematical modeling. Then, read at least three of the news articles below. Note: you need to be on campus or use the UA VPN to access the full text of some of these articles.

• Rapid Response Could Have Curbed Foot-and-Mouth Epidemic by M. Enserink
• Disease control: Virtual plagues get real by V. Gewin
• African swine fever outbreak alarms wildlife biologists and veterinarians by Erik Stokstad
• U.K. expands kill zone for badgers in fight against bovine TB, sparking controversy by Erik Stokstad
• Italy’s olive crisis intensifies as deadly tree disease spreads by Alison Abbott
• Animal testing outperformed by computer models by Alfie Gleeson

Then answer the following questions; include a discussion of the articles (with proper references) you read in your argumentation.

• Do you believe mathematical models should be used to make decisions that impact society?
• What criteria do you think such models should satisfy, if they are to be used for policy-making or public health purposes?

Your essay should be about 1 page long, typed, and written in proper English. It will be graded for content as well as for writing style, spelling, and grammar.

Please place a single file in PDF format with your work in the D2L Assignment Submission Folder called Homework 1.