A ST 523 Biological Sampling
Fall 2011
This syllabus is a guideline for the course and not a contract. As such, its terms may be altered when doing so is, in
the opinion of the instructor, in the best interests of the class.
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.
2.
3.
Burnham, K.P., D.R. Anderson, and J.L. Laake. 1980. Estimation of Density from Line Transect
Sampling of Biological Populations. Wildlife Monographs, 72.
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.
Pollock, K.H., J.D. Nichols, C. Brownie, and J.E. Hines. 1990. Statistical Inference for CaptureRecapture 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 - 1:10-2:25 p.m. Business Complex Rm. 343
INSTRUCTOR:
Dr. Bill Gould
OFFICE HOURS:
TBD
Office GU 211
Telephone 6-3986
OR 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 September 2. The last day to drop with
a W is October 11. The Final Exam is scheduled on Tuesday, Dec. 6, from 1:00-3:00pm.
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:
http://www.warnercnr.colostate.edu/~gwhite/software.html. A user’s manual is also downloadable at
Evan Cooch’s website: www.phidot.org/software/mark/docs/book.
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 Student Accessibility Services (SAS) at
646-6840 (V) or 646-1918 (TTY) located in Corbett Center, Room 244 or email at
sas@nmsu.edu with any questions you may have on student issues related to the Americans with
Disabilities Act (ADA and/or Section 504 of the Rehabilitation Act). Students requesting
accommodations and/or services relating to a disability may seek assistance from the SAS Office
located in Corbett Center, Room 244. All medical information will be treated confidentially.
Questions regarding NMSU's Non-discrimination Policy and discrimination complaints
should be referred to Gerard Nevarez, Office of Institutional Equity, 575-646-3635
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.
2.
3.
4.
Definitions of variables of interest and description of measurement methods for Frequency, Density, Cover,
Biomass
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
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
Line and Point Intercept methods
Exam #1 Sept 22- 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 October 27?
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
7.
Removal Methods (two-sample and multiple samples), Generalized Removal Model (goodness of
fit test), Catch Per Unit Effort (Leslie, DeLury, ML methods)
Exam #3 December 6, Tuesday, 1:00-3:00pm, BC 343
Reading Assignments for A 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: http://liberes.nmsu.edu, 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 http:// www.phidot.org/software/mark/docs/book
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
http:// www.phidot.org/software/mark/docs/book
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
8. Elzinga, C.L. and A.G. Evenden. [Compilers] 1997. Vegetation monitoring: an annotated bibliography.
Technical report, Forest Service, USDA
9. Elzinga, C.L., D.W. Salzer, and J.W. Willoughby. 1998. Measuring and Monitoring Plant Populations.
BLM Technical Report 1730-1, Denver Colorado.
10. Grieg-Smith, P. 1983. Quantitative Plant Ecology. University of California Press: Berkeley.
11. Krebs, C.J. 1989. Ecological Methodology. HarperCollins: New York..
12. Ludwig, J.A. and J.F. Reynolds. 1988. Statistical Ecology. Wiley: New York.
13. Manly, B.F.J., L.L. McDonald, and D.L. Thomas. 1993. Resource Selection by Animals. Chapman &
Hall: London
14. 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.
15. Seber, G.A.F. 1982. The Estimation of Animal Abundance. MacMillan: New York.
16. Thompson, S.K. 1992. Sampling. Wiley: New York.
17. Johnson, D.H. 2002. The importance of replication in wildlife research. Journal of Wildlife
Management 66:919-932.