Kenneth H. Pollock
231 David Clark Labs
515-3514 pollock@unity.ncsu.edu
A statistics methods sequence at the level of ST 511-512 or permission of instructor
Office Hours
M W 1.30-2.30pm and Tu 2.00-3.00pm or by appointment.
Exam Dates-All exams will be take home exams.
Exam 1 - Tuesday Sept 30,2008 Handout
Exam 2 - Tuesday November 4, 2008 Handout
Please do not try Mr Harris's approach on my exams!!
Class Times Tu/Th 5.45pm-7.00pm DCL 102.
Lecture 1
Estimation Notes
Finite Popn Sampling Notes from Design Class
Lecture 2
Lecture 3
Lecture 4
Lecture 5
From Distance list serve
Lecture 6
Lecture 7
Pollock Capture-Recapture Monograph
Lecture 8
MARK Notes
Lecture 9
Lecture 10
Lecture 11
Lecture 12
Lecture 13
Lecture 14
Lecture 15
Lecture 16
Lecture 17
Lecture 18
Lecture 19
Lecture 20 L Brooks
Lecture 21
Lecture 22-23
Lecture 23
Lecture 24
Lecture 25
Lecture 26
Lecture 27
Lecture 28 Presence Software
Set 1
Set 2
Set 3
Waterbird Paper for Homework 3.
Set 4
Set 5
Set 6 Use of MARK and CAPTURE
Set 7
Set 8
Set 9
Set 10
Set 11-Dec 2
Set 12-Dec 4
Set 12 Solution
Topic Choices :
Review of a topic; something related to your thesis research that has to do with sampling animal populations; simulation to study properties of an estimator for a particular sampling model; and others that you find interesting. All topics have to be approved by me. I want you to choose something of interest and benefit to you.
Timetable:
1. Title and Preliminary Abstract Sept 18, 2008
2. Rough Synopsis ( Table of Contents) October 7, 2008
3. Rough Draft of Paper November 18, 2008
4. Final Paper December 9, 2008 5pm or permission from me.
Structure:
Your paper will contain the following elements:
A detailed abstract of contents
A Table of Contents
Set of key Words
An Introduction
A Series of Sections which give the details
A Discussion and Suggestions for Future Research
Literature Cited
Tables
Figures
Length and Substance:
I require approximately 15 pages of text ( double spaced ) with extra pages of Tables, Figures, Literature Cited etc. This is a substantial task so do not wait until the last minute to get started. This can be a very valuable experience for you as writing is neglected in our graduate programs. Employers always state that it is a critical skill they desire in prospective employees..
Williams, Nichols and Conroy (2002). Analysis and Management of Animal Populations. Academic Press. ISBN 0-12-754406-2
James D. Nichols has made enormous
contributions
to population estimation in many different areas. He is also a
tremendous supporter and friend to those lucky enough to have worked
with him.
Mike Conroy, Ken Williams, Jim Nichols
celebrating
the book completion in serious style.
Williams is an expert on adaptive
management
and Head of the Coop Unit Program in USGS. Conroy has made important
contributions
to band return models and other population estimation methods. He is an
expert in adaptive management methods and population biology.
Hwk 20
Exam 1 20
Exam 2 20
Exam 3 20
Project 20
TOTAL 100
General
Ricker, W. E. (1958). Handbook of computations for biological statistics of fish populations. Fisheries Research Bulletin of Canada, Bulletin 119. 300pp.
Lancia, R. A., Nichols, J. D., and Pollock, K. H. (1994). Estimating the number of animals in wildlife populations in T.A. Bookout, ed. Research and management techniques for wildlife and habitats. Fifth ed. The Wildlife Society, Bethesda, MD, 215-253. (Introductory)
Seber (1982). The Estimation of Animal Abundance and Related Parameters.Macmillan, New York.( Very detailed).
Schwarz, C. J., and Seber, G. A. F. (1999). A review of estimating animal abundance III, Statistical Science 14, 427-456.
Burnham, K. P., and Anderson, D. R. (2002). Model Selection
and Inference:
A Practical Information Theoretic Approach, New York: Springer-Verlag.
Pollock,
K. H., Marsh, H., Bailey, L. L., Farnsworth, G.
L., Simons, T. L., and Alldredge, M. W. (2004) Separating components of
detection probability in abundance estimation: An overview with diverse
examples. In W. L Thompson Ed. Sampling Rare and Elusive Species:
Concepts,
Designs and Techniques for Estimating Population Parameters. Island
Press,
Dave Anderson, Ken Burnham and Gary
White from
Colorado State University have made enormous contributions to
population
estimation
in so many areas. One special mention
should
be the creation of MARK!
A marvellous program which has
revolutionised
the field!
Sampling Theory
Cochran, W. G ( 1967) Sampling Techniques, Wiley, New York.
Thompson, S. K. (2002) Sampling, 2nd Edition, Wiley, New York.
Angler Surveys and Survey Methodology
Pollock, K. H., Jones, C. M. and Brown, T.
L.
(1994). Angler Surveys and their application to fisheries
management.
American Fisheries Society Special Publication 25, Bethesda, Maryland.
Cynthia Jones
Aerial Surveys
Pollock, K. H., and Kendall, W. L. (1987). Visibility bias
in aerial surveys: A review of estimation procedures. Journal of
Wildlife Management 51, 502-510.
Adaptive Sampling
Thompson, S. K. and Seber, G.
A.F.(1996)
Adaptive Sampling, 2nd Edition, Wiley, New York.
Distance Sampling Methods
S.T. Buckland, D.R. Anderson, K.P. Burnham, J.L Laake, D.L. Borchers and L. Thomas (2001).Introduction to Distance Sampling:Estimating Abundance of Biological Populations. Oxford University Press.
Alpizar-Jara, R. & Pollock, K.H. (1996). A combination line transect and capture- recapture sampling model for multiple observers in aerial surveys, Journal of Environmental and Ecological Statistics 3, 311-327.
Alpizar-Jara, R.(1997). Assessing assumption violations in line transect sampling. Ph D Dissertation, Biomathematics Program, North Carolina State University, Raleigh, North Carolina, U. S. A.
Arnason, A.N. & Schwartz, C.J. (1999). Using POPAN-5 to analyse banding data. Bird Study, 46, S157-S168.
Borchers, D. L., Zucchini, W., and Fewster, R. M.. (1998).
Mark-Recapture
Models for Line Transect Surveys, Biometrics, 54, 1207-1220.
Stephen
Buckland
David Borchers
Alldredge, M. R. (2004). Avian Point Count Surveys: Estimating Components of the Detection Process.(Biomathematics/Zoology) <>Ph D Thesis, NCSU.
Farnsworth, G., Pollock, K.H., Nichols, J. D., Simons, T. R., Hines, J. E., and Sauer, J. R. (2002). A removal model for estimating the detection probability during point counts divided into time intervals. The Auk, 119: 414-425.
Capture-Recapture Methods
Monographs
Burnham, K. P., Anderson, D. R., White, G. C., Brownie, C., and Pollock, K. H. (1987). Design and Analysis Methods for Fish Survival Experiments based on Release-Recapture. American Fisheries Society Monographs 5, Bethesda, Maryland. (ISSN 0362-1715).
Lebreton, J.-D., Burnham, K. P., Clobert, J., and Anderson, D. R. (1992). Modelling Survival and Testing Biological Hypotheses Using Marked Animals: A Unified Approach with Case Studies, Ecological Monographs, 62, 67-118.
Otis, Burnham, White and Anderson (1978).Statistical Inference from Capture Data on Closed Animal Populations.Wildlife Monograph 62.
Pollock, K. H., Nichols, J. D., Brownie, C., and Hines, J. E. (1990). Statistical Inference for Capture-Recapture Experiments, Wildlife Society Monographs (No. 107).
White, G.C., Anderson, D.R., Burnham,
K.P. and
Otis, D.L. (1982). Capture-Recapture and Removal Methods for Sampling
Closed
Populations. Los Alamos National Lab, LA-8787-NERP, Los Alamos, New
Mexico,
USA.
Cooch , E. Online book on program MARK.
An invaluable resource!
Some Classic Papers
Laplace, P.S. (1786). Sur les naissances, les mariages et les morts in Memoires de L’Academie Royale des Sciences, 1783, Paris, pp. 693-702.
Petersen, C.G.J. (1896). The yearly immigration of young plaice into the Limfjiord from the German Sea, Report of Danish Biological Station 6, 1-48.
Lincoln, F.C. (1930). Calculating Waterfowl Abundance on the Basis of Banding Returns. United States Department of Agriculture Circular, No. 118.
Schnabel, Z.E. (1938). The estimation of the total fish population of a lake. American Mathematical Monthly 45: 348-52.
Jackson, C. H. N. (1939). The analysis of an animal population. Journal of Animal Ecology, 8, 238-246.
Jackson, C. H. N. (1940). The analysis of a tsetse fly population:I. Annals of Eugenics 10,332-369.
Jackson, C. H. N. (1944). The analysis of a tsetse fly population:II. Annals of Eugenics 12, 176-205.
Jackson, C. H. N. (1948). The analysis of a tsetse fly population:III. Annals of Eugenics 14, 91-108.
Fisher, R. A. and Ford, E. B. (1947). The spread of a gene in natural conditions in a colony of the moth Panaxia dominula. Heredity , 1, 143-174.
Chapman, D.G. (1951). Some properties of the hypergeometric distribution with applications to zoological sample censuses, University of California Publication in Statistics 1, 131-160.
Bailey, N.T.J. (1951). On estimating the size of mobile populations from recapture data. Biometrika 38: 293-306.
Cormack, R.M. (1964). Estimates of survival from the sighting of marked animals, Biometrika 51, 429-38.
Darroch, J.N. (1958). The multiple-recapture census I. Estimation of a closed population. Biometrika 45: 343-59.
Darroch, J.N. 1959. The multiple-recapture census: II. Estimation when there is immigration or death. Biometrika 46:336-351.
Jolly, G. M. (1965). Explicit Estimates From Capture-Recapture Data With Both Death and Immigration – Stochastic Model, Biometrika, 52, 225-247.
Seber, G. A. F. (1965), A Note on the Multiple Recapture Census, Biometrika, 52, 249-259.
Manly, B.F.J. and Parr, M.J. (1968). A new method of estimating population size, survivorship and birth rate from capture-recapture data. Transactions of the Society for British Entomology 18, 81-89.
Robson, D. S. (1969). Mark-recapture methods of population estimation. Pages 120-140 in N. L. Johnson and H. Smith, Jr., eds. New developments in survey sampling. John Wiley and Sons, New York, New York.
Fienberg, S. E. (1972). The multiple-recapture census for closed populations and incomplete contingency tables. Biometrika, 59,591-603.
Arnason, A.N. 1973. The estimation of population size, migration rates and survival in a stratified population. Researches on Population Ecology 15:1-8.
Carothers, A.D. (1973). Capture-recapture methods applied to a population with known parameters. Journal of Animal Ecology 42: 125-46.
Pollock, K.H. (1975). A K-sample tag-recapture model allowing for unequal survival and catchability. Biometrika 62, 577-583.
Burnham, K. P., and Overton, W. S. (1978). Estimation of the Size of a Closed Population When Capture probabilities Vary Among Animals, Biometrika, 65, 625-633.
Pollock, K.H. (1981). Capture-recapture models allowing for age-dependent survival and capture rates. Biometrics 37, 521-529.
Pollock, K. H. (1982), A Capture-Recapture Design Robust to Unequal Probability Capture, Journal of Wildlife Management, 46: 752-757.
White, G.C. 1983. Numerical estimation of survival rates from band recovery and biotelemetry data. J. Wildl. Manage. 47:716-728.
Pollock, K. H., Hines, J. E. and Nichols J.N. (1985). Goodness of fit tests for open capture-recapture models. Biometrics 41, 399-410.
Huggins, R. M. (1989). On the Statistical Analysis of Capture Experiments, Biometrika, 76, 133-140.
Chao, A. (1989). Estimating population size for sparse data in capture-recapture experiments. Biometrics 45: 427-38.
Huggins, R. M. (1991). Some Practical Aspects of a Conditional Likelihood Approach to Capture Experiments, Biometrics, 47, 725-732.
Important Recent Papers (Incomplete)
Arnason, A.N. & Schwartz, C.J. (1999). Using POPAN-5 to
analyse
banding data. Bird Study, 46, S157-S168.
Bailey,
L. L., T. R. Simons, and K.
H. Pollock.(2004). Estimating
detectability parameters for plethodon salamanders using the robust
capture-recapture design. Journal of Wildlife Management, 68:
1-13.
Bailey,
L.
L., T. R. Simons, and K. H. Pollock.(2004). Spatial and temporal
variation in
detection probability of plethodon salamanders using the robust
capture-recapture design. Journal of
Wildlife Management, 68: 14-24.
Barker, R. J. (1997). Joint Modelling of Live Recapture, Tag-Resight and Tag-Recovery Data , Biometrics, 53, 666-677.
Brownie, C., Hines, J. E., Nichols, J. D., Pollock, K. H., and Hestbeck, J. B. (1993). Capture-recapture studies for multiple strata including non-Markovian transition probabilities. Biometrics 49, 1173-1187.
Burnham, K. P. (1993). A Theory for Combined Analysis of Ring Recovery and Recapture Data. Pages 199-213, In J.-D. Lebreton and P. M. North editors. Marked Individuals in the Study of Bird Population. Birkhauser. Verlag, Basel, Switzerland.
Chao, A. (2001). An overview of closed capture-recapture models. Journal of Agricultural, Biological and Environmental Statistics 6: 158-75.
Chao, A., Lee, S.-M., and Jeng, S. L. (1992). Estimating population size for capture-recapture data when capture probabilities vary by time and individual animal. Biometrics, 48, 201-216.
Dorazio and Royle. (2003). Mixture models for estimating the
size of a closed population when capture rates vary among individulas.
Biometrics, 59, 351-364.
Hestbeck, J. G., Nichols, J. D., and Malecki, R. A. (1991). Estimates of movement and site fidelity using mark-resight data of wintering Canada Geese, Ecology, 72,523-533.
Kendall, W. L., Pollock, K. H., and Brownie, C. (1995). A likelihood-based approach to capture-recapture estimation of demographic parameters under the Robust design. Biometrics , 51, 293-308.
Kendall, W. L., and Nichols, J. D.(1995). On the use of secondary capture-recapture samples to estimate temporary emigration and breeding proportions. Journal of Applied Statistics 22, 751-762.
Kendall, W. L. , Nichols, J. D. and Hines. J. E. (1997). Estimating temporary emigration using capture-recapture data with Pollock’s robust design. Ecology , 78, 563-578.
Lebreton, J.-D., and Pradel, R. (2001). Multi-stratum capture-recapture models: modeling incomplete capture histories. Journal of Applied Statistics This Volume.
Lee, S.-M., and Chao, A. (1994). Estimating Population Size via Sample Coverage for Closed Capture-Recapture Models, Biometrics, 50, 88-97.
Link, W. A. (2003). Nonidentifiability of population size from
capture-recapture data with heterogeneous detection probabilities.
Biometrics, 59, 1123-1130.
Nichols, J. D., Sauer, J. R., Pollock, K. H., and Hestbeck, J. B. (1992). Estimating transition probabilities for stage based population projection matrices using capture-recapture data. Ecology 73, 306-312.
Nichols, J. D., and Hines, J. E. (2001) Approaches for the direct estimation of lambda and demographic contributions to lambda using capture-recapture data.. Journal of Applied Statistics
Norris, J. L., and Pollock, K. H. (1995). Capture-recapture model Mbh: Bivariate MLE of capture-recapture distribution and resulting model selection. Journal of Environmental and Ecological Statistics 2, 305-313.
Norris, J. L., and Pollock, K. H. (1996). Nonparametric maximum likelihood estimators for population size under two closed capture-recapture models with heterogeneity. Biometrics 52, 639-649.
Pine,
W. E., Pollock, K. H., Hightower, J. E.,
Kwak, T. J., and Rice, J. A. (2003). A review of tagging methods for
estimating
fish population size and components of mortality. Fisheries
28: 10-23.
Pledger, S. (2000). Unified Maximum Likelihood Estimates
for
Closed
Capture-Recapture Models Using Mixtures, Biometrics, 56, 443-450..
Pledger, S., Pollock, K.
H.,Norris, J. L. (2003). Open Capture-recapture models with
heterogeneity. 1.
Cormack-Jolly-Seber model. Biometrics 59: 786-794.
Pollock, K. H. (2000). Capture-Recapture Models, Journal of the American Statistical Association, 95, 293-296.
Pradel, R. (1996), Utilization of Capture-Mark-Recapture for the Study of Recruitment and Population Growth Rate, Biometrics, 52, 703-709.
Schwarz, C. J., and Arnason, A. N. (1996), A General Methodology for the Analysis of Capture-Recapture Experiments in Open Populations, Biometrics, 52, 860-873.
White, G. C., and Burnham, K. P. (1999), Program MARK: Survival Estimation from Populations of Marked Animals, Bird Study, 46, S120-S139.
Yip, P. S. F.(1991). A martingale estimating equation for a capture-recapture experiment in discrete time, Biometrics, 47, 1081-1088.
Pollock, Burnham, Pledger, Wellendorf
and Norris
have all worked on capture-recapture models.
Picture taken at a recent ASA meeting.
Carl Schwarz
Paul Yip
Anne Chao, Paul Yip and Postgraduate Students
Bill Kendall
Removal or Depletion and Catch-Effort Methods
Gould, W. R., and Pollock, K. H. (1997). Catch-effort maximum likelihood estimation of population parameters. Canadian Journal of Fisheries and Aquatic Science 54, 890-897.
Gould, W. R., and Pollock, K. H. (1997). Catch-effort estimation of population parameters under the robust design. Biometrics 53, 207-216.
White, G.C., Anderson, D.R., Burnham, K.P. and Otis, D.L. (1982). Capture-Recapture and Removal Methods for Sampling Closed Populations. Los Alamos National Lab, LA-8787-NERP, Los Alamos, New Mexico, USA.
Zippin, C. (1956). An evaluation of the removal method of estimating animal populations, Biometrics 12, 163-189.
Bill Gould
Selective Removal Methods ( Change in Ratio)
Paulik and Robson (1969). Statistical calculations for change-in-ratio estimators of population parameters. Journal of Wildlife Management 33, 1-27.
Hoenig, J. M., and Pollock, K. H. (1998). Index-removal estimators. Encyclopedia of Statistics Update Volume 2, p. 342-346.
Lancia, R. A., Nichols, J. D., and Pollock, K. H. (1994). Estimating the number of animals in wildlife populations in T.A. Bookout, ed. Research and management techniques for wildlife and habitats. Fifth ed. The Wildlife Society, Bethesda, MD, 215-253.
Pollock, K. H., and Hoenig, J. M. (1998). Change-in-ratio estimators. Encyclopedia of Statistics Update Volume 2, p. 109-112.
Nest Survival and Radio-Telemetry Survival Methods
Mayfield, H.(1961). Nesting success calculated from exposure.Wilson Bulletin, 73, 255-261.
Pollock, K. H., and Cornelius, W. L. (1988). A distribution free nesting survival model. Biometrics 44, 397-404.
Trent, T. T., and Rongstad, O. J. (1974), Home Range and Survival of Cottontail Rabbits in Southwestern Wisconsin, Journal of Wildlife Management, 38, 459-472.
Heisey, D. M., and Fuller, T. K. (1985). Evaluation of Survival and Cause Specific mortality Rates Using Telemetry Data, Journal of Wildlife Management, 49, 668-674.
Pollock, K. H., Winterstein, S. R., Bunck, C. M., and Curtis, P. D. (1989). Survival analysis in telemetry studies: the staggered entry design. Journal of Wildlife Management 53, 7-15.
Pollock, K. H., Winterstein, S. R., and Conroy, M. J. (1989). Estimation and analysis of survival distributions for radio-tagged animals. Biometrics 45, 99-109.
Pollock, K. H., Bunck, C. M., Winterstein, S. R., and Chen, C. L. (1995). A capture-recapture survival analysis model for radio-tagged animals. Journal of Applied Statistics, 22, 661-672.
Hightower, J. E., Jackson, J. R.,and Pollock, K. H. (2001). Using telemetry methods to estimate natural and fishing mortality of striped bass in Lake Gaston NC. Transactions of the American Fisheries Society, 130, 557-567.Pollock, K. H., Jiang, H. and Hightower, J. E. (2004). Combining Radio-Telemetry and Fisheries TaggingModels to Estimate Fishing and Natural Mortality Rates. Transactions of the American Fisheries Society.
Joe Hightower
Tag-Return Models
Brownie, C., Anderson, D. R., Burnham, K. P., and Robson, D. S. (1985), Statistical Inference From band-Recovery Data: A handbook (2nd ed, Resource publication 156), Washington, DC: Fish and Wildlife Service, U.S. Department of the Interior.
Cavell Brownie
Hoenig, J. M., Barrowman, N. J., Hearn, W. S. and Pollock, K. H. (1998). Multiyear tagging studies incorporating fishing effort data. Canadian Journal of Fisheries and Aquatic Sciences 55, 1466-1476.
Hoenig, J. M., Barrowman, N. J.,
Pollock, K. H.,
Brooks, E. N. and Hearn, W. S., and Polacheck, T. (1998).
Models
for tagging data that allow for incomplete mixing of newly tagged
animals.
Canadian Journal of Fisheries and Aquatic Sciences 55, 1477-1483.
John Hoenig
Bill Hearn
Pollock, K. H., Hearn, W. S., Hoenig, J. M., and Calingaert, B. (2001). Estimation of reporting rate 1: An evaluation of the reward tagging method of estimating tag reporting rate and fishing and natural mortality. North American Journal of Fisheries Management, 21: 521-532.
<>Pollock, K. H., Hearn, W. S., Hoenig, J. M., and Calingaert, B. (2002). Estimation of reporting rate 2: A review and comparison of different methods of estimating tag reporting rate. North American Journal of Fisheries Management, 22: 727-736.
Hearn, W.S., Hoenig, J. M., Pollock, K. H. and Hepworth, D. (2003) Estimation of reporting rate 3: Use of planted tags in a multi-component fishery. North American Journal of Fisheries Managemen,t 23: 66-77.
1. Introduction to Estimation of Animal Abundance (Ch 12.1-12.2)
2. Statistical Inference Background (Ch 4)
3. Finite Sampling Background (Ch 5)
4. Estimating Abundance Based on Counts (Ch 12)
Note: Separation of detection probability into available and detection given available components. This is new research.
5. Estimating Abundance with Distance Methods (Ch 13)
6. Estimating Abundance for Closed populations Using Capture-Recapture Sampling (Ch 14)
7. Estimation of Demographic Parameters (Ch 15)
8. Estimation of Survival Rates with Band Recoveries (Ch 16)
9. Estimating Survival, Movement, and Other State Transitions with Mark-Recapture Methods (Ch 17)
10. Estimating Abundance & Recruitment with Mark-Recapture Methods (Ch 18)
11. Combining Closed & Open Mark-Recapture : The Robust Design. (Ch 19)
12. Estimation of Community Parameters (Ch 20).
13. Estimation of Proportion of Area Occupied (not in book). Notes Provided.
Some very important computer software will be demonstrated during the semester. In particular MARK, CAPTURE, and DISTANCE. There are links below to the locations where this software can be accessed.