Welcome to Ecological Modeling (BI382) at Colby College

A message from quarantine

This is where you may access the large number of relevant changes to the course syllabus and schedule and plans on moving forward for remote learning through quarantine during a pandemic. The major changes to our syllabus are number any types of assignments, which I show below in the Assessment and grade assignment section. I also have changed office hours to accomodate your scheudles; note the changes in the Office hours section below.

Statement of principles

Statement of Principles for the Remainder of Spring 2020 Semester for Ecological Modeling (BI382):

  1. Neither you nor I signed up for this
    • Neither of us signed up knowing the crisis that we’d be facing, not for the physical distancing, not of the abrupt end of our physical lives together on campus
    • Neither of us signed up for an online class, not for teaching remotely, not for learning remotely, not for mastering new technologies, not for varied access to learning materials
  2. The humane option is the best option during a global crisis
    • We are going to prioritize supporting each other as humans
    • We are going to prioritize simple solutions that make sense for the most
  3. We cannot just do the same thing online that we did in class
    • Some assignments are no longer effective (e.g., real-time/synchronous exchange of ideas during class discussions)
    • Some expectations are no longer reasonable (e.g., Case Study Presentations)
    • Some learning goals are no longer as feasible or as important
  4. We will foster intellectual nourishment, social connection, and personal accommodations through
    • Accessible asynchronous content for diverse access, timezones, and contexts
    • Optional synchronous discussion to learn together and combat isolation (Slack and Zoom)
  5. We will remain flexible and adjust to the situation
    • Nobody know where this is going and how we’ll need to adapt
    • Everybody needs support and understanding in this unprecidented moment

Download as .pdf

Adapted from Brandon Bayne, UNC Chapel Hill (<a href = https://twitter.com/brandonbayne/status/1239336664176250880">Tweet</a>)

Course description

Ecological Modelling is a course that is designed to help students learn theory and methods in mathematical and computational ecology. Collectively, these types quantitative approaches are central to the science of ecology for understanding, predicting, and making inferences about ecological patterns and processes. Both classic and contemporary topics will be covered, with an emphasis on using modern tools to analyze and present theory and data.

Learning outcomes

After taking this course as successful student should:

  1. Have gained an appreciation of the art and science of modeling.
  2. Be versed in theoretical ecology, which includes understanding ecological topics on single-species population dynamics, structured population dynamics, spatial dynamics, two-species population dynamics, and multi-species dynamics.
  3. Be versed in theoretical ecology, which includes understanding and applying mathematical/analytical tools and topics on equilibrium, stability, chaos, and stochasticity.
  4. Be able to build, analyze, and present ecological models using the R programming language and environment. This includes understanding and use of R data structures, functional programming, libraries for simulation and analysis of ecological models, and dynamic reports/documents using R Markdown Documents.
  5. Be able to (re)create a scientific model. The “Remodeling Project” will include assessing and choosing a peer-reviewed model that can feasibly be recreated, recreate the model, and critique the model.

Professor information

Dr. Christopher M. Moore
Email: cmmoore
Office: Olin 216
Office phone: 207-859-5746

Meetings for discussions and labs

Pandemic meetings

Optional during classtime: M, 1—4:00 PM; TR, 9:30—10:45 AM on Zoom: link

Pre-pandemic meetings

Labs: M, 1—4:00 PM, in Davis 308
Discussions: TR, 9:30—10:45 AM, in Miller 205

Office hours

Pandemic office hours

Optional office hours: Zoom link
M: 10 AM–noon EDT
T: 8–10 AM EDT
T: 1–3 PM EDT
W: 4–6 PM EDT

Pre-pandemic office hours

T: 1–3 PM in Olin 216
R: 7–9 AM in Olin 216
F: 1–3 PM at Mary Low Coffeehouse (With the exception of 28 Feb. and 13 March, where the Biology Deptartment seminar is from 1–2 in Olin 01 and Office Hours will be from 2–4 PM.)

Text

Assessment and grade assignment

Pandemic assessment and grade assignment

I am cutting the quizzes and problem sets (except for disease), but everything else will be graded the same. This means that the new sum of the course is 0.723. That will be the denominator for

Assignments Each No. Proportion of the course (old) Approx. proportion of the course (/0.723)
Problem sets 0.035 6 0.210 0.290
Quizzes (individual) 0.011 4 0.044 0.061
Quizzes (group) 0.011 4 0.044 0.061
Lab experiments 0.040 1 0.040 0.055
Lab reports 0.030 4 0.120 0.166
Remodeling project 0.240 1 0.240 0.332
Participation 0.025 1 0.025 0.035

Pre-pandemic

Assignments Each No. Proportion of the course
Problem sets 0.035 9 0.315
Quizzes (individual) 0.011 10 0.110
Quizzes (group) 0.011 10 0.110
Lab experiments 0.040 2 0.080
Lab reports 0.030 4 0.120
Remodeling project 0.240 1 0.240
Participation 0.025 1 0.025

Attendance

Role will not be taken, but regular attendance is necessary for you to succeed in this course.

Titles and names

Students are often curious about how to address their professors. I am comfortable with Dr. Moore, Professor Moore, or Chris. What’s most important to me is that we create a culture of mutual respect in the classroom. As a sign of respect to you I will, by default, address you by your first name. Should you have preferred way of being addressed (Mx. last name, nickname, etc.), I encourage your to communicate that to me.

Participation

This success of the class (group) is contingent upon each student (individual) coming prepared and eager to engage with the course material and one another. Of course I will employ methods to muster enthusiasm and energy, but to be clear, this is a group effort. I ask that you do your best to come to class prepared by not only having read, but doing your best to understand to the extent that if called upon, you could recall the material from the reading in addition to stating your’s own analysis of the reading’s strengths, weaknesses, and higher-level analogies (e.g., relating concepts to other areas of basic and applied science).

The quality and the quantity of participation will be taken into account. That is, I fully encourage you to participate, but I’d like for a somewhat uniform distribution of substantive discussion. In addition, an egalitarian approach is encouraged to better facilitate exchange of ideas. Nobody is interested in group members dominating discussion. If you are one that tends to monopolize discussion, try to engage others, as this is—at least—as important as the matter at hand and is a skill that is greatly underrated and can really boost the level of discussion. If you are one that does not participate, please realize that your input is important to all of us! We are all intelligent and insightful, and engagement and input by all is how we will better understand the topic.

Overall, let’s just have fun learning, which is presumably why we are all here. Having a fun time playing ideological ping-pong (not dodge ball) with each other will only harbour growth and learning. Ecological theory can be abstract, conceptually challening, and a technical subject that lends itself greatly to creative and alternative views and approaches. In addition, ecological theory and modeling is a very applied topic, so I am certain that what we cover will touch upon each each of your scientific interests in some way.

Academic integrity

Honesty, integrity, and personal responsibility are cornerstones of a Colby education and provide the foundation for scholarly inquiry, intellectual discourse, and an open and welcoming campus community. These values are articulated in the Colby Affirmation and are central to this course. You are expected to demonstrate academic honesty in all aspects of this course. If you are clear about course expectations, give credit to those whose work you rely on, and submit your best work, you are highly unlikely to commit an act of academic dishonesty.

Academic dishonesty includes, but is not limited to: violating clearly stated rules for taking an exam or completing homework; plagiarism (including material from sources without a citation and quotation marks around any borrowed words); claiming another’s work or a modification of another’s work as one’s own; buying or attempting to buy papers or projects for a course; fabricating information or citations; knowingly assisting others in acts of academic dishonesty; misrepresentations to faculty within the context of a course; and submitting the same work, including an essay that you wrote, in more than one course without the permission of the instructors.

Academic dishonesty is a serious offense against the college. Sanctions for academic dishonesty are assigned by an academic review board and may include failure on the assignment, failure in the course, or suspension or expulsion from the College.

Athletic participation

While Colby College is supportive of athletic participation by its students, academics takes priority over athletics. Both NCAA and Colby rules prohibit missing class for practices. In the case of overlapping commitments between class and athletic competitions, the student must meet with the professor as soon as possible to discuss these overlaps. The student may request permission to miss class and make up the missed work; the instructor has final authority either to grant or to withhold permission

Sexual misconduct/Title IX statement

Colby College prohibits and will not tolerate sexual misconduct or gender-based discrimination of any kind. Colby is legally obligated to investigate sexual misconduct (including, but not limited to sexual assault and sexual harassment).

If you wish to speak confidentially about an incident of sexual misconduct, please contact Colby Counseling Services (207-859-4490) or the Director of the Gender and Sexual Diversity Program, Emily Schusterbauer (207-859-4093).

Students should be aware that faculty members are considered responsible employees; as such, if you disclose an incident of sexual misconduct to a faculty member, they have an obligation to report it to Colby’s Title IX Coordinator. “Disclosure” may include communication in-person, via email/phone/text, or through class assignments.

To learn more about sexual misconduct or report an incident, visit http://www.colby.edu/sexualviolence/.

Download this page as a .pdf, last updated 21 January 2019