Spring 2016
Modeling for Field Biologists (Biol 6301)
Instructor: Ken Schmidt
Tuesday and Thursday 3:30-4:50
Lecture Room: Biology 405
Course Description:
This is a workshop course in which I will teach some basics of modeling ecology and evolution for the novice who is unfamiliar with mathematical techniques, a programming language (I will use Matlab in this course, which is free to TTU students), or simply doesn’t know where to get started.
This course should appeal to students that have had introductory classes in ecology and evolution but who have a small ‘mathematical toolbox’ and/or no or little programming experience. I will use limited calculus and linear algebra as applied to ecological models, but do not intend to teach these as proper subjects. While familiarity with these fields of math may be useful it is not necessary.
Expected Learning Outcomes: After completion of the course students will:
Course Outline
Section 1: An Intro to using Matlab and some basic models: Logistic growth, Lotka-Volterra competition, diet-choice/patch use behavior, ideal-free distribution and habitat selection (marginal value theorem and isoclines/isolegs).
Section 2: Population growth in spatial and temporally variable environments (arithmetic vs. geometric growth)
Section 3: Stage structured growth and population projection (life tables and eigenvalues). An introduction to using and manipulating arrays in Matlab.
Section 4: Signal detection theory. We’ll do some optimization and Bayesian updating applied to ecological questions, including decision-making in uncertain environments.
Section 5: Two Allee effects: the phenomenological and the mechanistic (using the Solve function, Poisson chipmunks)
Section 6: Building individual-based models – an introduction to more complex models that follow individuals’ choices and outcomes.
Methods of assessing learning outcomes:
There will be no exams; however, there will be a final project. Evaluations will be based solely on completion (or substantial progress) of an term assignment and regular 'weekly' assignments. You may work together on these projects, but each person must turn in individual weekly assignments. The term assignment
Special accommodation
ADA statement: Any student who, because of a disability, may require special arrangements in order to meet the course requirements should contact the instructor as soon as possible to make any necessary arrangements. Students should present appropriate verification from Student Disability Services during the instructor’s office hours. Please note instructors are not allowed to provide classroom accommodations to a student until appropriate verification from Student Disability Services has been provided. For additional information, you may contact the Student Disability Services office in 335 West Hall or 806-742-2405.
Statement about observance of religious holidays: A student who intends to observe a religious holy day should make that intention known in writing to the instructor prior to the absence. A student who is absent for the observance of a religious holy day shall be allowed to take an exam or complete an assignment scheduled for that day within a reasonable time after the absence.
Academic Honesty: It is the student’s responsibility to conduct him/herself in a civil manner while in the classroom. Please consult the university policy on and academic honesty (OP 34.12) and civility.
Modeling for Field Biologists (Biol 6301)
Instructor: Ken Schmidt
Tuesday and Thursday 3:30-4:50
Lecture Room: Biology 405
Course Description:
This is a workshop course in which I will teach some basics of modeling ecology and evolution for the novice who is unfamiliar with mathematical techniques, a programming language (I will use Matlab in this course, which is free to TTU students), or simply doesn’t know where to get started.
This course should appeal to students that have had introductory classes in ecology and evolution but who have a small ‘mathematical toolbox’ and/or no or little programming experience. I will use limited calculus and linear algebra as applied to ecological models, but do not intend to teach these as proper subjects. While familiarity with these fields of math may be useful it is not necessary.
Expected Learning Outcomes: After completion of the course students will:
- Be familiar with some basic models of ecology (e.g., population growth and projection), animal behavior (diet choice, habitat selection), and other ecological principles
- Have a basic understanding of the nature of programming in Matlab
- Be familiar with a variety of modeling approaches so students can identify and have the confidence in using modeling in their own system
Course Outline
Section 1: An Intro to using Matlab and some basic models: Logistic growth, Lotka-Volterra competition, diet-choice/patch use behavior, ideal-free distribution and habitat selection (marginal value theorem and isoclines/isolegs).
Section 2: Population growth in spatial and temporally variable environments (arithmetic vs. geometric growth)
Section 3: Stage structured growth and population projection (life tables and eigenvalues). An introduction to using and manipulating arrays in Matlab.
Section 4: Signal detection theory. We’ll do some optimization and Bayesian updating applied to ecological questions, including decision-making in uncertain environments.
Section 5: Two Allee effects: the phenomenological and the mechanistic (using the Solve function, Poisson chipmunks)
Section 6: Building individual-based models – an introduction to more complex models that follow individuals’ choices and outcomes.
Methods of assessing learning outcomes:
There will be no exams; however, there will be a final project. Evaluations will be based solely on completion (or substantial progress) of an term assignment and regular 'weekly' assignments. You may work together on these projects, but each person must turn in individual weekly assignments. The term assignment
Special accommodation
ADA statement: Any student who, because of a disability, may require special arrangements in order to meet the course requirements should contact the instructor as soon as possible to make any necessary arrangements. Students should present appropriate verification from Student Disability Services during the instructor’s office hours. Please note instructors are not allowed to provide classroom accommodations to a student until appropriate verification from Student Disability Services has been provided. For additional information, you may contact the Student Disability Services office in 335 West Hall or 806-742-2405.
Statement about observance of religious holidays: A student who intends to observe a religious holy day should make that intention known in writing to the instructor prior to the absence. A student who is absent for the observance of a religious holy day shall be allowed to take an exam or complete an assignment scheduled for that day within a reasonable time after the absence.
Academic Honesty: It is the student’s responsibility to conduct him/herself in a civil manner while in the classroom. Please consult the university policy on and academic honesty (OP 34.12) and civility.