WLF 448: Fish & Wildlife Population Ecology

Fall 2010

Lab 1: INTRODUCTION

I. Teaching Assistant:

II. Location and Meeting Time of Lab Sections:

III. About the Lab

A. Purpose of Lab

The purpose of the laboratory is to give you experience in the quantitative aspects of population ecology that are essential for both understanding the dynamics of populations and for managing populations of fish and wildlife. At the end of this course, you should be able to wisely use models and data to address pressing questions involving the management and conservation of fish and wildlife populations.

B. Computer programs will be used to:

1. Explore the quantitative methods for estimating population parameters such as abundance, density, survival, and growth rate,

2. Illustrate principles of population ecology (e.g., population growth, population regulation, demography, species interactions), and

3. Demonstrate practical uses of concepts presented in lecture.

C. Problem Sets (20 points each)

You will receive weekly problem sets or assignments worth 20 points each. Each lab assignment is due the following week at the beginning of class. For each day that an assignment is late, 2 points will be deducted from the respective grade up to a maximum of one half the points.

In most cases, your answers to the problem set will consist of :

1. Hard copy (printout) of data and/or command-file,

2. Condensed or edited output (in some cases, output can be emailed to your TA), and

3. Answers to questions.

NOTE: Output for problem sets should be neat and organized. If a specific format is required for an exercise, it will be outlined in the problem set.  However, all answers to discussion questions should be typed, double-spaced, and consist of complete sentences and thoughts. Points will be deducted for repeated misspelling, incomplete sentences, and poor grammar. Consult with each other on program applications but work independently otherwise (i.e., do your own work when answering questions and interpreting results).

D. Software

Ecological software used in this lab will be available on the UI network under s:\courses\wlf448 or in a few cases under lab software. Note: you cannot run the software from the s:\ drive. You must copy the program and data files to your personal network directory on a network drive. You can do this by dragging and dropping the directory to your drive space or a flash drive in a USB port. A few programs used in this lab are DOS-based software and, therefore, will not run properly in the Windows environment. Consequently, you will need to learn basic DOS commands for file management, editing, and running software in some instances.

NOTE:  Some of the software used in this class may appear to be "vintage" software.  However, much of it still is currently in use among fish and wildlife biologists.  These programs were developed by biologists, not by software engineers, so user interfaces are not necessarily well defined and occasional bugs are encountered.  Most biologists have limited computer programming skills and are often are paid by public funds, so software development is not generally a priority.  Please recognize those limitations while working with the software.

It is a good idea to backup your files on a regular basis, especially your data and document files. Every computer in McClure 214A has a USB port on the front for plugging in a flash drive or portable hard disk, which may be your best option for backing up large or many files. Flash drives and portable hard disks can be purchased from the bookstore. If you want to copy files for use on a personal computer at home or elsewhere, you will need to provide your own transportable media for that purpose.

IV. General Format of Labs

1. 15-20 min. review/discussion of the previous week's topic and assignment.  This is a student presentation by 1-2 individuals each week.

2. 30-45 min. introduction to the current lab topic. Note: lab topics may not always coincide with lecture topics. When this occurs, the TA may need to spend more time discussing background information and theory.

3. Short break

4. Demonstration of computer program/simulation

5. In-class exercise

6. Problem set (due the following week)

V. Attendance

Students are responsible for all material covered in labs, including material presented by TAs, Dr. Oleyar, and in student presentations.

If you will miss a lab or will arrive late or leave early due to other commitments, please inform the TA a priori. In such cases, it is your responsibility to get notes from another student. Do not expect the TA to spend an hour of their office time repeating the lab presentation or demonstration that you missed.  Arrange in advance to attend another lab time if absolutely necessary.

VI. Student Presentation (25 points)

A. Purpose

The purpose of the student presentation is to give each student experience in: (1) organizing and preparing technical information, (2) making oral presentations, (3) answering technical questions, and (4) using audio-visual equipment. Presentations should be similar in nature to those presented at professional conferences.  In addition, the presentations will serve as a concise review of the previous week's topic and methodology, and provide an opportunity to discuss and debate answers to the problem set.

NOTE: Some students in the past have viewed the review session/student presentations as a "waste of time" because the problem set was already completed. Furthermore, students often do not like to ask challenging questions of other students because they know they will have to present a topic at a later date. However, asking questions and discussing completed work can be a valuable educational tool for both students and working professionals as this repeated thinking and discussion about a topic makes it easier to remember the details later. We encourage you to view the student presentations as a chance for class discussion and debate about the merits of a topic. Please ask questions of the student presenters, the TA, and Dr. Oleyar.

B. Groups:

You will work alone or together in groups of 1-3 students, depending on class size. Each week, 1 topic will be reviewed. The TA will assign students to groups and topics. Groups and assigned topics will be announced at the beginning of Lab #2, and a list will be posted on this web site (see Student Presentations). Each member of the group is expected to contribute to the presentation and discussion (i.e., it should be a group effort). However, how you divide up the preparation work and actual presentation is up to you. All members of the group should be able to address questions posed by the audience.

C. Topics:

Student presentations will cover the material from the previous week's lab (see Lab Schedule). There will be 1 presentation per week, beginning with Lab 3 during the week of 7 September 2011.

D. Format:

Presentations will be 10 minutes long (12 minutes maximum), with an additional 5 minutes for questions and answers (total time = 15-17 minutes). This is similar to time limits for presentations at professional meetings. The TA will act as a moderator to make sure each group stays within their allotted presentation time and the class discussion does not dwell on any 1 question for too long. Because your time is limited, you must present the information in a concise, organized manner (i.e., only the most pertinent information should be presented).

How you organize your presentation is up to each group. However, we recommend the following approach:

1. Introduction (e.g., brief review of main ecological concepts or principles),

2. Problem identification (i.e., brief description of problem set),

3. Methodology (e.g., describe data collection, analysis methods, assumptions, etc.),

4. Results (usually presented as tables and/or figures), and

5. Discussion and Conclusions (e.g., interpretation of results, validity of results, potential applications, discussion questions, new questions, etc.).

Presentations should be in the form of a Powerpoint presentation (*.ppt) to be shown on the screen at the front of the classroom.  Other visual aids can include the use of an overhead projector and a white board.  If you choose to use other media (e.g., slide projector or TV), you will be responsible for arranging to have those materials on hand at the time of your presentation.

NOTE:  When preparing your presentation, make sure your text is large enough so that people can read it from the back of the room when it is projected on the screen.  Also, avoid slides that consist solely of extensive text or are too "busy".  Bullet lists and sentence fragments are more useful than paragraphs and complete sentences in a presentation.  Tables and figures should be easy to understand and only include data relevant to the specific item you will be discussing on that slide.  Consult with the TA if you have questions about preparing presentations, but do not wait until 1 hour before your scheduled presentation to do so.

E. Grading

The presentation will be worth 25 points. You will be graded on content and organization of the presentation, presentation skills, contribution to group effort, and participation in class discussions (both as a presenter and as a member of the audience). Do not get uptight about this presentation -- just make sure that your group is organized and prepared, and you contribute equally to the presentation. Use it as an opportunity to learn and experiment!  Grading on the quality of the slides will be more lenient during the early presentations, as students learn what is expected of them, and will be more stringent as the semester progresses.

VII. UI Computing Network

1. You will need a UI student account (contact the ITS HELP Desk in the Commons Bldg., Phone: 885-HELP).

2. You must log in before each class so that you can follow along with the instructor and save your work.

3. Log off when finished (click on the Start button to log off or shut down).

VIII. Accessing and Running Class Software

    1.    Log in as you would on any UI computer.

    2.    Copy appropriate files from s: drive to your personal network drive:

Open the "My Computer" icon. Click on the "Shared (S:)" network drive. Click on "Courses" folder.  Scroll down to "WLF448" and click on it. All class software folders should be visible. To copy files, drag the desired folders (e.g., "CAPTURE") to your student account folder or other removable media. You also can perform these same operations in Windows Explorer which is available under Start - Programs - Accessories at the bottom left of your screen.

    3.    Notes:

(a) You should only need to copy files once for each lab (but you may want to delete all files in your subdirectory and try the copy procedure again if the program fails to run properly and you cannot figure out the problem).

(b) Remember, you cannot run the software from the s: drive. You must copy it to your personal directory/subdirectory on a network drive in order to run it and save output.

(c) Keep your disk space organized.  Use subdirectories and standard file-naming conventions (e.g., *.inp for input files, *.out for output files, and *.txt for text files).

(d) Backup your files on a regular basis, especially your output and document files.

IX. Insights/Thoughts on Population Ecology Lab

1. In most cases, we will spend 1 lab-day on each topic and the corresponding estimation or simulation program. Obviously, this is not enough time to become totally familiar with the programs, their strengths and weaknesses, and the many options associated with certain programs. However, you will gain a working understanding of the various programs and estimation techniques, and will know where to go for more detailed information. In addition, you will learn to be a "problem solver" when it comes to running and applying ecological software to your specific population-ecology question.

2. Caveat: "If all factors were known for a population, understanding its dynamics would be straightforward... Population analysis often requires modeling of some sort, especially to bridge gaps in knowledge. A model is some abstraction of a real system that enables us to think more clearly about the real one... Modeling logically precedes estimation, because modeling can tell us which variables are important. Conversely, the availability of useable estimates often dictates the kind of model that can be constructed, so modeling and estimation go hand in hand" (Johnson 1994:419-420). However, output from computer modeling and/or estimation is only as good as the data that go into it. Careful consideration must be given to data collection, experimental design and/or sampling methodology, sample size, statistical and biological assumptions, knowledge gaps and uncertainty, validity of the estimates, and application of the results.

X. Wildlife 448 Lab Policy on Academic Honesty and Cheating

One of the purposes of Wildlife 448 is “to develop your quantitative skills and mastery of statistical methods, computer software, and simulation tools.”  A major portion of this goal will be accomplished by each student working independently through the lab exercises.  Therefore, we expect the Problem Set for each exercise to reflect your individual work.  Having said that, we fully expect and encourage you to share ideas, discuss problems with other students, and help each other make the software function, as this may be the best way to stimulate or solidify your own ideas.  This is very similar to what you would do in a professional setting as a fish or wildlife biologist.

There will be some labs for this class where the line between individual work and sharing ideas may be less clear.  The purpose of this policy is to help you make the distinction between acceptable collaboration (e.g., discussion of findings) and cheating (e.g., sharing of materials and collaboration on write-ups).

Unfortunately, a single definition is unlikely to include all situations of cheating and acceptable work.  When trying to decide whether something is cheating, consider how you would handle it in a professional setting.  Would you ask a colleague to do your analysis or interpret your results for you?  Would you ask a colleague to show you how to run a piece of software?  Would you discuss your findings with a colleague to see if they are valid?  Below, we have listed some examples of likely situations that we will use to decide if a student has cheated.

 If you have any questions about whether something is cheating or not, our advice is don’t do it or ask your TA.

 Students who cheat on lab exercises will receive a 0 for that exercise.  Repeat offenders will receive a 0 for the lab portion of their Wildlife 448 grade. 

XI.  In Class Exercise and Lab Assignment

Revised: 15 November 2011