EST 523 Biological Sampling

Spring 2008

TEXT: You will be required to read material from various journals, monographs and books, some of which you will be lent (listed below, they must be signed out and returned before receiving your final grade). Other readings will be on reserve at the old library (Branson)

1.Burnham, K.P., D.R. Anderson, and J.L. Laake. 1980. Estimation of Density from Line Transect Sampling of Biological Populations. Wildlife Monographs, 72.

2.White, G.C., D.R. Anderson, K.P. Burnham, and D.L. Otis. 1982. Capture-Recapture and Removal Methods for Sampling Closed Populations. Los Alamos Nat’l Lab.

  1. Pollock, K.H., J.D. Nichols, C. Brownie, and J.E. Hines. 1990. Statistical Inference for Capture-Recapture Experiments. Wildlife Monographs, 107.

Optional: Analysis and Management of Animal Populations. 2002. Williams, Nichols and Conroy. Academic Press. This is at the very least a great reference book that I recommend buying and keeping. Many of the topics listed for reading at the library are contained within this book, but is more comprehensive than our class time allows.

TIME AND LOCATION: Tuesday and Thursday - 2:35-3:50 p.m.Business Complex Rm. 343

INSTRUCTOR:Dr. Bill GouldOffice GU 211 Telephone 6-3986

OFFICE HOURS:2:00-3:00 Wednesday, 4:00-5:00 ThursdayOR by appointment

PREREQUISITES:EST 505 or EST 502 or consent of instructor.

Course Description:This course is designed to acquaint the student with some of the more popular methods of measuring vegetation and estimating the abundance and survival rates of animal populations. Emphasis is placed on understanding the conceptual and statistical basis underlying the estimation techniques. Hands on use of software (e.g., program MARK) will also be emphasized.

Grade: Three exams will count 30% each toward your final grade. All grades on tests must be contested within one week of reception. Class participation and completion of HW will count for 10% of your grade.

Grades will be assigned as follows: A: 100 – 90; B: 89 – 80; C: 79 – 70; D: 69 – 60; F: < 60

A grade of C or higher must be obtained to receive an ‘S’ rating for an S/U rating.

Important Dates: The last day to drop the course without record is February 1. The last day to drop with a W is March 10, 2008. The Final Exam is scheduled on Thursday, May 8, from 3:30-5:30pm.

Class Attendance & Participation: Attendance is not mandatory, but strongly encouraged. If you miss class, it is your responsibility to recover the material you missed. No make-up exams will be given. Your comments and questions are encouraged during class. Questions alert me to any misunderstandings that you have as a class. If a concept is not clear to you, it likely is not clear to others either, so please speak up! In addition, I will inquire about your insight and experiences. This classroom interaction will be a welcome break from listening to me. Note, however, that behavior that is disruptive to the academic environment will not be tolerated from any student.

The schedule of material to be covered this semester is located on a separate sheet. This schedule lists the material and readings to be covered. Please read the material prior to class. The lectures will be more interesting and helpful if you have already read the material. It is your responsibility to read the material! Program MARK will be available on the machines in the classroom, but I suggest you download it on your own machine from Gary White’s web page: A user’s manual is also downloadable at Evan Cooch’s website:

Academic Misconduct is not tolerated and will be subject to disciplinary action (see guidelines in student handbook). Academic misconduct includes but is not limited to cheating or knowingly assisting another student in committing an act of cheating or plagiarism. This does not mean you cannot work on homework together, but copying is not allowed. A grade of zero will be assigned to any persons/assignments resulting from academic misconduct. (Refer to the guidelines for academic misconduct in the Student Handbook for further details)

ADA statement: If you have or think you may have a disability that interferes with your academic progress, you are encouraged to contact the Services for Students with Disabilities at 646-6840 (V) or 646-1918 (TTY) or to discuss this on a confidential basis with your instructor. Services for students with disabilities are located in Garcia Annex, Room 102. Current and appropriate documentation will be required in order to receive services. It is your responsibility to inform either your instructor or SSD representative in a timely manner if services/accommodations provided are not meeting your needs.

If you have a condition which may affect your ability to exit safely from the premises in an emergency or which may cause an emergency during class, you are encouraged to discuss any concerns with the instructor and/or Michael Armendariz, SSD Coordinator. Feel free to call Ms. Angela Velasco, Interim EEO/ADA and Employee Relations Director at 646-3333 with any questions about the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation Act of 1973. All medical information will be treated confidentially.

Study Skills:Reading the text prior to class, effective note-taking and regular completion of the homework problems are essential for performing well in the class. If needed, the Center for Learning Assistance (646-3136) can help you to develop the necessary study skills for your college education.

Course Outline:

Introduction: General Principles of Scientific Research (modified from Krebs 1989), The 20 commonest sampling sins (Taken from Sutherland 1996).

Overview of Statistical Terminology: parameter, statistic, sampling distribution, bias, precision, consistency, accuracy (as measured by mean squared error), etc.

Overview of simple random, stratified and systematic sampling.

Plant sampling:

1.Definitions of variables of interest and description of measurement methods for Frequency, Density, Cover, Biomass

2.Quadrat Sampling (includes strip transects) Consideration of plant distribution and quadrat size and shape, Perimeter–to-area ratios, optimal quadrat size (variance estimation under distributional assumptions) Goodness of Fit tests for certain spatial patterns

3.Plotless Methods (estimation of mean area, biases depending on spatial patterns, Goodness of fit tests for spatial pattern), Closest individual method, Nearest Neighbor, Quarter Method

4. Line and Point Intercept methods

Exam #1 Feb 28- Take home component is critique of Etchberger and Krausman (1997, Wildlife

Society Bulletin 25:604-609)

Overview of likelihood functions, Maximum Likelihood Estimation, Goodness of Fit Testing, Model Selection Methods including Information Theoretic approaches, model averaging, etc.

5.Capture-Recapture

Closed Population Models (Petersen model, assumptions and effects of violations), Multiple

Marking Period Models MT, MB, MH, etc. (emphasis on likelihood functions and estimation, model

selection and performance, estimator averaging) Program CAPTURE and MARK hands on.

Exam #2 April 3?

Open Population Models (assumptions, parameter and statistic definitions), Cormack-Jolly-Seber Model,

Robust Design, Program MARK hands on.

6.Distance sampling (assumptions, design considerations, detectability function, fundamental models, probability density construction, variance estimation including bootstrap and jackknife, sample size estimation) Program DISTANCE demonstration

  1. Removal Methods (two-sample and multiple samples), Generalized Removal Model (goodness of

fit test), Catch Per Unit Effort (Leslie, DeLury, ML methods)

Exam #3 May 8, Thursday, 3:30-5:30pm, BC 343

Reading Assignments for E ST 523

Please read the sections prior to class. The lectures will be more interesting and helpful if you have already read the material. It is your responsibility to read the material!

The articles are available electronically. You can access them by connecting to the Web and going to the html address: then select ‘Look up Electronic Reserves and Course Materials’. Then select my name as the instructor (Gould, William) and then select EST 523. At this point, you enter a password: biosamp and click ‘Accept’. you will then see the articles listed in numeric order.

You may have to rotate the articles in the reader for them to be displayed correctly and of course, you can print them out for reading as well.It is recommended that you use Internet Explorer (as opposed to Netscape) to access files via the Web. A free copy (on a burned CD) is available from the Computer Center (ICT) rm. 143

1) Pages 61-69 in Williams et al. Analysis and Management of Animal Popns. 2002.

1b) Skalski, J.R. 1987. SRS in a circular plot: Ecology (handout), P. 749.

2) Bonham, C. 1989. Measurements for Terrestrial Vegetation. Pp. 1-15 on Historical overview.

3) Higgins et al. in Bookhout, T.A. (ed). Research and Management Techniques…1994. Pp. 567-581, 587-588 on Vegetation sampling.

4) Krebs. C. 1989. Ecological Methodology.Pp. 64-71 on Quadrat sampling.

P) Johnson, R. R. and Higgins, K.F. 1998. Wetlands 18:329-334 (handout)

5) Brummer et al. 1994. Journal of Range Management 47:84-89.

6) Krebs. 1989. Spatial distribution, testing Goodness-of-Fit: P. 72-81.

7) Bonham, 1989. Plotless methods: P. 148-165. And Krebs. P. 136-141.

8) Mueller-Dumbois and Ellenburg, 1974. Line-intercept, variable-radius method: P. 90-92, 101-106.

9) Etchberger and Krausman 1997. Evaluation of methods in desert ecosystem, WSB, P. 604-609

10a) Anderson, D.R. 2001. The need to get the basics right in wildlife field studies,WSB P. 1294-1297.

11) Lancia et al. in Bookhout. 1994. Animal abundance overview: P. 215-234.

P) Notes from Anderson and Burnham course or sections 4.1 and 4.2 in Williams et al. 2002.

Chapter 1, Program MARK: A gentle introduction. E. Cooch and G.C. White. 2005.

Go to

P) Gould and Pollock 2002. Capture-recapture methods (overview). Encyclopedia of Environmetrics.

P) White et al. 1982. Introduction to capture-recapture estimation: P. 1-11, 26-32 (middle)

OR pages 289-296 in Williams et al. 2002 (Web)

P) White et al. 1982. Capture-recapture: closed population models P. 45-76.

OR pages 296-314 in Williams et al. 2002. (Web)

P) Pollock et al. 1990. Capture-recapture: open population models P. 18-30.

OR pages 495-508 in Williams et al. 2002 (Web)

P) Pollock et al. 1990. Robust design: P. 56-61. OR pages 523-538 in Williams et al. 2002. (Web)

P) Kendall, W.L. 2001. The robust design for capture-recapture studies: analysis using program MARK. Pages 357-360 in R. Field, R.J. Warren, H. Okarma, and P.R. Sievert, editors. Wildlife, land and people: priorities for the 21st century. Proceedings of the Second International Wildlife Management Congress. The Wildlife Society, Besthesda, MD, USA.

P) White et al. 2001. Advanced features of program MARK. Pages 368-377 in R. Field, R.J. Warren, H. Okarma, and P.R. Sievert, editors. Wildlife, land and people: priorities for the 21st century. Proceedings of the 2nd International Wildlife Management Congress. The Wildlife Society, Besthesda, MD, USA.

Chapter 3, Program MARK: A gentle introduction. E. Cooch and G.C. White. 2005. Go to

and/or White, G.C. and K.P. Burnham. 1999. Program MARK: survival estimation from populations of marked animals. Bird Study 46 Supplement:120-138 (Web).

P) indicates that I will provide the material.

I may also provide articles by Engeman 2003 and Anderson 2003 on value of indices, Stanley and Burnham 1998 on closed estimator selection and averaging,

Relevant References

1. Anderson, D.R. and K. P. Burnham. 1998. Model Selection and Inference. Springer-Verlag: New York.

2. Bonham, C. 1989. Measurements for Terrestrial Vegetation. Wiley & Sons: New York.

3. Bookhout, T.A. [Editor] 1994. Research and Management Techniques for Wildlife and Habitats,

5th Edition, The Wildlife Society, Allen Press: Bethesda.

5. Brownie, C., D.R. Anderson, K.P. Burnham, and D.S. Robson. 1985. Statistical inference from band recovery data-a handbook. Second Edition, U.S. Fish and Wildlife Service Res. Pub. 156.

6. Buckland, S.T., D.R. Anderson, K.P. Burnham, and J.L. Laake. 1993. Distance Sampling: Estimating Abundance of Biological Populations. Chapman and Hall: London.

7. Diggle, P.J. 1983. Statistical Analysis of Spatial Point Patterns. Academic Press: London

  1. Elzinga, C.L. and A.G. Evenden. [Compilers] 1997. Vegetation monitoring: an annotated bibliography. Technical report, Forest Service, USDA
  1. Elzinga, C.L., D.W. Salzer, and J.W. Willoughby. 1998. Measuring and Monitoring Plant Populations. BLM Technical Report 1730-1, DenverColorado.

10. Grieg-Smith, P. 1983. Quantitative Plant Ecology. University of California Press: Berkeley.

11. Krebs, C.J. 1989. Ecological Methodology. HarperCollins: New York..

  1. Ludwig, J.A. and J.F. Reynolds. 1988. Statistical Ecology. Wiley: New York.
  1. Manly, B.F.J., L.L. McDonald, and D.L. Thomas. 1993. Resource Selection by Animals. Chapman & Hall: London
  1. Otis, D.L., K.P. Burnham, G.C. White, and D.R. Anderson. 1978. Statistical Inference from

Capture Data on Closed Animal Populations. Wildlife Monographs, 62, The Wildlife Society.

  1. Seber, G.A.F. 1982. The Estimation of Animal Abundance. MacMillan: New York.
  1. Thompson, S.K. 1992. Sampling. Wiley: New York.
  1. Johnson, D.H. 2002. The importance of replication in wildlife research. Journal of Wildlife Management 66:919-932.