Disease dynamics in wild populations: Modeling and estimation: A review

Journal of Ornithology

Volumn 152, Issue SUPPL. 2, 2012, Pages 485-509

  Cooch, Evan G ^a   Conn, Paul B ^b   Ellner, Stephen P ^a   Dobson, Andrew P ^c   Pollock, Kenneth H ^d  

^a Department of Obstetrics Gynecology   (United States)

^b SOUTHEAST FISHERIES SCIENCE CENTER   (United States)

^c PRINCETON UNIVERSITY   (United States)

^d NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Detection probability; Disease models; Mark recapture; Multi state models; Parameterization; Time series; Uncertain states

Indexed keywords

DETECTION METHOD; DISEASE INCIDENCE; DISEASE PREVALENCE; ESTIMATION METHOD; INFECTIOUS DISEASE; INFECTIVITY; MARK-RECAPTURE METHOD; MARKOV CHAIN; MODEL TEST; NUMERICAL MODEL; ORNITHOLOGY; PARAMETERIZATION; SPATIAL VARIATION; TEMPORAL VARIATION; TIME SERIES ANALYSIS;

EID: 84859268950     PISSN: 21937192     EISSN: 21937206     Source Type: Journal    
DOI: 10.1007/s10336-010-0636-3     Document Type: Review

References (189)

1. Altizer S, Nunn C, Thrall P, Gittleman J, Ezenwa V, Pulliam J, Pedersen A, Dobson A, Poss M, Cunningham A, Antonovics J, Jones K (2003) Social organization and disease risk in mammals: integrating theory and empirical studies. Annu Rev Ecol Evol S 34: 517-547.
2. Altizer S, Hochachka W, Dhondt AA (2004) Seasonal dynamics of mycoplasmal conjunctivitis in eastern north american house finches. J Anim Ecol 73: 309-322.
3. Altizer S, Dobson AP, Hosseini P, Hudson P, Pascual M, Rohani P (2006) Seasonality and the dynamics of infectious diseases. Ecol Lett 9: 467-484.
4. Anderson RM, May RM (1992) Infectious diseases of humans, dynamics and control. Oxford University Press, Oxford.
5. Andersson H, Britton T (2000) Stochastic epidemic models and their statistical analysis, lecture notes in statistics, vol 151. Springer, New York.
6. Arnason AN (1973) The estimation of population size, migration rates, and survival in a stratified population. Res Popul Ecol 15: 1-8.
7. Barker RJ, White GC (2004) Towards the 'mother-of-all-models': customized construction of the mark-recapture likelihood function. Anim Biodivers Conserv 27: 177-185.
8. Barker RJ, Cooch EG, Schwarz CJ (2002) Discussion comments on: approaches for the direct estimation of λ and demographic contributions to λ using capture-recapture data. J Appl Stat 29: 569-572.
9. Beal MJ, Ghahramani Z, Rasmussen CE (2002) The infinite hidden Markov model. In: Dietteric T, Becker S, Ghahramani Z (eds) Advances in neural information processing systems 14. MIT Press, Cambridge.
10. Becker NG (1989) Analysis of infectious disease data. Monographs on statistics and applied probability. Chapman and Hall, London.
11. Benyoussef L, Carincotte C, Derrod S (2008) Extension of higher-order HMC modeling with application to image segmentation. Digit Signal Process 18: 849-860.
12. Besbeas P, Freeman SN, Morgan BJT, Catchpole EA (2002) Integrating mark-recapture-recovery and census data to estimate animal abundance and demographic parameters. Biometrics 58: 540-547.
13. Besbeas P, Freeman SN, Morgan BJT (2005) The potential of integrated population modelling. Aust NZ J Stat 47: 35-48.
14. Bjørnstad O, Grenfell BT (2005) Hazards, spatial transmission and timing of outbreaks in epidemic metapopulations. Environ Ecol Stat 15: 265-277.
15. Borchers DL, Buckland ST, Zucchini W (2002) Estimating animal abundance-closed populations. Statistics for biology and health. Springer, Berlin.
16. Borysiewicz RS, Morgan BJT, Hénaux V, Bregnballe T, Lebreton JD, Gimenez O (2009) An integrated analysis of multisite recruitment, mark-recapture-recovery and multisite census data. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, UK, pp 579-591.
17. Bradshaw CJA, Brook BW (2005) Disease and the devil: density-dependent epidemiological processes explain historical population fluctuations in the Tasmanian devil. Ecography 28: 181-190.
18. Bretó C, He D, Ionides EL, King AA (2008) Time series analysis via mechanistic models. Ann Stat 3: 319-348.
19. Brooks SP, King R, Morgan BJT (2004) A Bayesian approach to combining animal abundance and demographic data. Anim Biodivers Conserv 21: 515-529.
20. Brown BW, Monfort A, van Dijk H (eds) (1993) Econometric inference using simulation techniques. Wiley, New York.
21. Brownie C, Hines JE, Nichols JD, Pollock KH, Hestbeck JB (1993) Capture-recapture studies for multiple strata including non-Markovian transitions. Biometrics 49: 1173-1187.
22. Bruno JF, Ellner SP, Vu I, Kim K, Harvell CD (2010) Impacts of aspergillosis on sea fan coral demography: modeling a moving target. Ecol Monogr (in press).
23. Buckland ST, Newman KB, Thomas L, Koesters NB (2004) State-space models for the dynamics of wild animal populations. Ecol Model 171: 157-175.
24. Buckland ST, Newman KB, Fernández C, Thomas L, Harwood J (2007) Embedding population dynamics models in inference. Stat Sci 22: 44-58.
25. Burnham KP (1993) A theory for combined analysis of ring recovery and recapture data. In: Lebreton JD, North P (eds) Marked individuals in the study of bird population. Birkhauser, Basel, pp 199-213.
26. Burthe S, Telfer S, Begon M, Bennett M, Smith A, Lambin X (2008) Cowpox virus infection in natural field vole Microtus agrestis populations: significant negative impacts on survival. J Anim Ecol 77: 110-119.
27. Buzby M, Neckels D, Antolin MF, Estep D (2008) Analysis of the sensitivity properties of a model of vector-borne bubonic plague. J R Soc Interface 5: 1099-1107.
28. Caley P, Marion G, Hutchings MR (2009) Assessment of transmission rates and routes, and the implications for management. In: Delahey RJ, Smith GC, Hutchings MR (eds) Management of disease in wild mammals. Springer, New York, pp 31-51.
29. Cam E (2009) Contribution of capture-mark-recapture modeling to studies of evolution by natural selection. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 83-129.
30. Cam E, Link WA, Cooch EG, Monnat JY, Danchin E (2002) Individual covariation in life-history traits: seeing the trees despite the forest. Am Nat 159: 96-105.
31. Cappé O, Moulines E, Rydén T (2005) inference in hidden Markov models. Springer series in statistics. Springer, New York.
32. Caswell H (2001) Matrix population models-construction, analysis, and interpretation, 2nd edn. Sinauer, Sunderland.
33. Cauchemez S, Ferguson NM (2008) Likelihood-based estimation of continuous-time epidemic models from time-series data: application to measles transmission in london. J R Soc Interface 5: 885-889.
34. Cauchemez S, Valleron AJ, Boelle PY, Flahault A, Ferguson NM (2008) Estimating the impact of school closure on influenza transmission from sentinel data. Nat Biotechnol 452: 750-756.
35. Challenger WO, Schwarz CJ (2009) Mark-recapture Jolly-Seber abundance estimation with classification uncertainty. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 827-844.
36. Chao A, Huggins RM (2005) Modern closed-population capture-recapture models. In: Amstrup SC, McDonald TL, Manly BFJ (eds) Handbook of capture-recapture analysis. Princeton University Press, Princeton, pp 58-86.
37. Chao A, Tsay PK, Lin SH, Shau WY, Chao DY (2004) The applications of capture-recapture models to epidemiological data. In: D'Agostino RB (eds) Statistical methods in clinical studies, tutorials in biostatistics, vol 1. Wiley, New York, pp 31-66.
38. Childs DZ, Rees M, Rose KE, Grubb PJ, Ellner SP (2004) Evolution of size-dependent flowering in a variable environment: construction and analysis of a stochastic integral projection model. Proc R Soc Lond B 271: 425-434.
39. Ching WK, Fung ES, Ng MK (2003) Higher-order hidden Markov models with applications to DNA sequences. In: Intelligent data engineerings and automated learning, lecture notes in computer science, Springer, Berlin, pp 535-539.
40. Choisy M, Rohani P (2006) Harvesting can increase the severity of wildlife disease epidemics. Philos Trans R Soc Lond B 273: 2025-2034.
41. Choquet R, Rouan L, Pradel R (2009) Program E-SURGE: a software application for fitting multievent models. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 845-866.
42. Chowell G, Rivas AL, Hengartner NW, Hyman JM, Castillo-Chavez C (2006) The role of spatial mixing in the spread of foot-and-mouth disease. Prev Vet Med 73: 297-314.
43. Clark JS, Bjørnstad O (2004) Population time series: process variability, observation errors, missing values, lags, and hidden states. Ecol Lett 85: 3140-3150.
44. Clark JS, Gelfland AE (2006) A future for models and data in environmental science. Trends Ecol Evol 21: 375-380.
45. Cochran ME, Ellner SP (1992) Simple methods for calculating age-based life history parameters for stage-structured populations. Ecol Monogr 62: 345-364.
46. Conn PB, Cooch E (2009) Multistate capture-recapture analysis under imperfect state observation: an application to disease models. J Appl Ecol 46: 486-492.
47. Conner MM, McCarty CW, Miller MMW (2000) Detection of bias in harvest-based estimates of chronic wasting disease prevalence in mule deer. J Wildl Dis 36: 691-699.
48. Craft ME, Hawthorne PL, Packer C, Dobson AP (2008) Dynamics of a multihost pathogen in a carnivore community. J Anim Ecol 77: 1257-1264.
49. Daley DJ, Gani J (2001) Epidemic modelling: an introduction. Cambridge University Press, Cambridge.
50. Delahay, R, Smith, G, Hutchings, M (eds) (2009) Management of disease in wild mammals. Springer, New York.
51. de Castro F, Bolker BM (2005) Mechanisms of disease-induced extinction. Ecol Lett 8: 117-126.
52. Dethlefsen C, Lundbye-Christensen S, Christensen AL (2009) SSPIR: State Space Models in R. http://CRAN. R-project. org/package=sspir, R package version 0. 2. 7.
53. de Jong M, Diekmann O, Heesterbeek H (1995) How does transmission of infection depend on population size?. In: Mollison D (eds) Epidemic models: their structure and relation to data. Cambridge University Press, Cambridge, pp 84-94.
54. de Jong M, Bouma A, Diekmann O, Heesterbeek H (2002) Modeling transmission: mass action and beyond. Trends Ecol Evol 17: 64.
55. Diekmann O, Heesterbeek JAP (2000) Mathematical epidemiology of infectious diseases: model buidling, analysis, and interpretation. Wiley series in mathematical and computational biology. Wiley, New York.
56. du Preez JA (1998) Efficient training of high-order hidden Markov models using first-order representations. Comput Speech Lang 12: 23-29.
57. du Preez JA, Weber DM (1999) The integration and training of arbitrary-order HMMs. Austr J Intel Inf Proc Sys (ICSLP98 Special Issue) 5: 261-268.
58. Dupuis J (1995) Bayesian estimation of movement and survival probabilities from capture-recapture data. Biometrics 82: 761-772.
59. Dupuis JA, Schwarz CJ (2007) A Bayesian approach to the multistate Jolly-Seber capture-recapture model. Biometrics 63: 1015-1022.
60. de Valpine P (2004) Better inferences from population-dynamics experiments using Monte Carlo state-space likelihood methods. Ecol Lett 84: 3064-3077.
61. de Valpine P, Hilborn R (2005) State-space likelihoods for nonlinear fisheries time-series. Can J Fish Aquat Sci 62: 1937-1952.
62. Easterling MR, Ellner SP, Dixon PM (2000) Size-specific sensitivity: applying a new structured population model. Ecol Lett 81: 694-708.
63. Efford MG (2004) Density estimation in live-trapping studies. Oikos 106: 598-610.
64. Efford MG, Borchers DL, Byrom AE (2009) Density estimation by spatially explicit capture-recpature: likelihood-based methods. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 255-269.
65. Ellner SP, Rees M (2006) Integral projection models for species with complex demography. Am Nat 167: 410-428.
66. Ellner SP, Rees M (2007) Stochastic stable population growth in integral projection models: theory and application. J Math Biol 54: 227-256.
67. Ellner SP, Bailey BA, Bobashev GV, Gallant AR, Grenfell BT, Nychka DW (1998) Noise and nonlinearity in measles epidemics: combining mechanistic and statistical approaches to population modeling. Am Nat 151: 425-440.
68. Engelbrecht H, du Preez JA (2009) Efficient backward decoding of high-order hidden Markov models. Pattern Recogn Lett 43: 99-112.
69. Faustino CR, Jennelle CS, Connolly V, Davis AK, Swarthout EC, Dhondt AA, Cooch EG (2004) Mycoplasma gallisepticum infection dynamics in a house finch population: seasonal variation in survival, encounter and transmission rate. J Anim Ecol 73: 651-669.
70. Fenichel EP, Horan RD (2007) Jointly-determined ecological thresholds and economic trade-offs in wildlife disease management. Nat Resour Model 20: 511-547.
71. Fine P, Clarkson J (1982) Measles in england and wales-1: an analysis of factors underlying seasonal patterns. Int J Epidemiol 11: 5-14.
72. Finkenstädt BF, Grenfell BT (2000) Time series modelling of childhood diseases: a dynamical systems approach. J R Stat Soc C 49: 187-205.
73. Fletcher D, Efford MG (2009) Effect of senescence on estimation of survival probability when age is unknown. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 1037-1053.
74. Gallant AR, Tauchen G (1996) Which moments to match?. Econ Theory 12: 657-681.
75. Gibson GJ, Renshaw E (1998) Estimating parameters in stochastic compartmental models using Markov chain methods. IMA J Math Appl Med 15: 19-40.
76. Gimenez O, Rossi V, Choquet R, Dehais C, Doris B, Varella H, Villa JP, Pradel R (2007) State-space modelling of data on marked individuals. Ecol Model 206: 431-438.
77. Gollery M (2008) Handbook of hidden Markov models in bioinformatics. Chapman and Hall, London.
78. Gouriéroux C, Monfort A (1996) Simulation-based econometric methods. CORE lectures. Oxford University Press, Oxford.
79. Grassly NC, Fraser C (2006) Seasonal infectious disease epidemiology. Proc R Soc Lond B 273: 2541-2550.
80. Grenfell B, Bjørnstad O, Kappey J (2001) Travelling waves and spatial hierarchies in measles epidemics. Nat Biotechnol 414: 716-723.
81. Grenfell BT, Dobson AP (1995) Ecology of infectious diseases in natural populations. Cambridge University Press, Cambridge.
82. Hansen L, Scheinkman J (1995) Back to the future: generating moment implications for continuous-time Markov models. Econometrika 63: 767-804.
83. Hawley DM, Davis AK, Dhondt AA (2007) Transmission-relevant behaviours shift with pathogen infection in wild house finches (Carpodacus mexicanus). Can J Zool 85: 752-757.
84. Hawley DM, Jennelle CS, Sydenstricker KV, Dhondt AA (2007) Pathogen resistance and immunocompetence covary with social status in house finches. Funct Ecol 21: 520-527.
85. Hedrich AW (1933) Monthly estimates of the child population 'susceptible' to measles, 1900-1931, baltimore, md. Am J Hyg 17: 613-636.
86. Hestbeck JB, Nichols JD, Malecki RA (1991) Estimates of movement and site fidelity using mark-resight data of wintering canada geese. Ecol Lett 72: 523-533.
87. Hochachka WM, Dhondt AA (2006) House finch (Carpodacus mexicanus) population- and group-level responses to bacterial disease. Ornithol Monogr 60: 30-43.
88. Hooker G, Xiao L (2009) CollocInfer: collocation inference for continuous-time dynamic systems. http://www. bscb. cornell. edu/hooker/CollocInfer, R package version 0. 0. 2.
89. Hosseini PR, Dhondt AA, Dobson AP (2004) Seasonality and wildlife disease: how season birth, aggregation and variation in immunity affect the dynamics of Mycoplasma gallisepticum in house finches. Proc R Soc Lond B 271: 2569-2577.
90. Hudson PJ, Rizzoli A, Grenfell BT, Hesterbeek H, Dobson AP (2002) The ecology of wildlife diseases. Oxford University Press, Oxford.
91. Ionides EI, Breto C, King AA (2006) Inference for nonlinear dynamical systems. Proc Natl Acad Sci USA 103: 18, 438-18, 443.
92. Jackson C (2009) msm: multi-state Markov and hidden Markov models in continuous time. http://CRAN. R-project. org/package=msm, R package version 0. 9. 2.
93. Jennelle CS, Cooch EG, Conroy MJ, Senar JC (2007) State-specific detection probabilities and disease prevalence. Ecol Appl 17: 204-167.
94. Joe M, Pollock KH (2002) Separation of survival and movement rates in multi-state tag-return and capture-recapture models. J Appl Stat 29: 373-384.
95. Keeling M, Bjørnstad O, Grenfell B (2004) Metapopulation dynamics of infectious diseases. In: Hanski I, Gaggiotti O (eds) Ecology, genetics, and evolution of metapopulations. Elsevier, Amsterdam, pp 415-445.
96. Keeling MJ, Gilligan CA (2000) Bubonic plague: a metapopulation model of a zoonosis. Proc R Soc Lond B 267: 2219-2230.
97. Keeling MJ, Rohani P (2007) Modeling infectious diseases in humans and animals. Princeton University Press, Princeton.
98. Kendall WL (2009) One size does not fit all: adapting mark-recapture and occupancy models for state uncertainty. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 765-780.
99. Kendall WL, Pollock KH, Brownie C (1995) A likelihood-based approach to capture-recapture estimation of demographic parameters under the robust design. Biometrics 51: 293-308.
100. Kendall WL, Langtimm CA, Beck CA, Runge MC (2004) Capture-recapture analysis for estimating manatee reproductive rates. Mar Mammal Sci 20: 424-437.
101. King AA, Ionides EL, Pascual M, Bouma MJ (2008) Inapparent infections and cholera dynamics. Nat Biotechnol 454: 877-U29.
102. King AA, Ionides EL, Bretó CM, Ellner S, Kendall B (2009) pomp: statistical inference for partially observed Markov processes (R package). http://pomp. r-forge. r-rproject. org.
103. Korobeinikov A, Maini PK, Walker WJ (2008) Non-linear transmission, mortality and stability of discrete-time infectious disease models. In: Wilson LB (eds) Mathematical biology research trends, mathematical biology research trends. Nova, Hauppauge, pp 237-259.
104. Koski T (2002) Hidden Markov models for bioinformatics computational biology, vol 2. Springer, New York.
105. Lachish S, Jones M, McCallum H (2007) The impact of disease on the survival and population growth rate of the Tasmanian devil. J Anim Ecol 76: 926-936.
106. Lande R (1987) Extinction thresholds in demographic models of territorial populations. Am Nat 130: 624-635.
107. Lawson AB (2009) Bayesian disease mapping-hierarchical modeling in spatial epidemiology. Interdisciplinary statistics. CRC, Boca Raton.
108. Lebreton JD (2009) Assessing density-dependence: where are we left?. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 19-41.
109. Lebreton JD, Pradel R (2002) Multistate recapture models: modeling incomplete individual histories. J Appl Stat 29: 353-369.
110. Link WA, Barker RJ (1994) Density estimation using the trapping web design: a geometric analysis. Biometrics 50: 733-745.
111. Link WA, Barker RJ (2005) Modeling association among demographic parameters in analysis of open population capture-recapture data. Biometrics 61: 46-54.
112. Link WA, Cooch EG, Cam E (2002) Model-based estimation of individual fitness. J Appl Stat 29: 207-224.
113. MacKenzie DI (2009) Getting the biggest bang for our conservation buck. Trends Ecol Evol 24: 175-177.
114. MacKenzie DI, Nichols JD, Hines JE, Knutson MG, Franklin AB (2003) Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecol Lett 84: 2200-2207.
115. MacKenzie DI, Bailey LL, Nichols JD (2004) Investigating species co-occurrence patterns when species are detected imperfectly. J Anim Ecol 73: 546-555.
116. MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Hines JE, Bailey LL (2005) Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier, Amsterdam.
117. MacKenzie DI, Nichols JD, Seamans ME, Gutierrez RJ (2009) Modeling species occurrence dynamics with multiple states and imperfect detection. Ecol Lett 90: 823-835.
118. Magle SB, McClintock BT, Tripp DW, White GC, Antolin MF, Crooks KR (2007) Mark-resight methodology for estimating population densities for praire dogs. J Wildl Manage 71: 2067-2073.
119. Marcos MM, Almaraz P, J A Sánchez-Zapata JA (2008) An emerging infectious disease triggering large-scale hyperpredation. PLoS One 3: e2307.
120. Maunder MN, Skaug HJ, Fournier DA, Hoyle SD (2009) Comparison of fixed effect, random effect and hierachical Bayes estimators for mark-recapture data using AD model builder. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 917-946.
121. Mausner JS, Bahn AK (1974) Epidemiology: an introductory text. Saunders, Philadeiphia.
122. McCallum H, Dobson A (1995) Detecting disease and parasite threats to endangered species and ecosystems. Trends Ecol Evol 10: 190-194.
123. McCallum H, Barlow N, Hone J (2001) How should pathogen transmission be modelled?. Trends Ecol Evol 16: 295-300.
124. McCallum H, Barlow N, Hone J (2002) Modelling transmission: mass action and beyond-response from McCallum, Barlow and Hone. Trends Ecol Evol 17: 64-65.
125. McCallum H, Tompkins DM, Jones M, Lachish S, Marvanek S, Lazenby B, Hocking G, Wiersma J, Hawkins CE (2007) Distribution and impacts of Tasmanian devil facial tumor disease. Econ Health 4: 318-325.
126. McClintock BT, White GC (2009) A less field-intensive robust design for estimating demographic parameters with mark-resight data. Ecol Lett 90: 313-320.
127. McClintock BT, White GC, Antolin MF, Tripp DW (2009) Estimating abundance using mark-resight when sampling is with replacement or the number of marked individuals is unknown. Biometrics 65: 237-246.
128. McClintock BT, White GC, Burnham KP, Pryde MA (2009) A generalized mixed effects model of abundance for mark-resight data when sampling is without replacement. In: DL Thomson EC, Conroy M (eds) Modeling demographic processes in marked populations. Springer, New York, pp 271-289.
129. McClintock BT, Nichols JD, Bailey L, MacKenzie DI, Kendall W, Fran (2010) Seeking a second opinion: uncertainty in disease ecology. Ecol Lett 13: 659-674.
130. Miller MW, Hobbs NT, Tavener SJ (2006) Dynamics of prion disease transmission in mule deer. Ecol Appl 16: 2208-2214.
131. Mochihashi D, Sumita E (2008) The infinite Markov model. In: Platt J, Koller D, Singer Y, Roweis S (eds) Advances in neural information processing systems 20. MIT Press, Cambridge, pp 1017-1024.
132. Morgan BJT (2007) A Kalman filter primer. J R Stat Soc A 170: 506.
133. Morvai G, Weiss B (2005) Order estimation of Markov chains. IEEE T Inform Theory 51: 1496-1497.
134. Murray KA, Skerratt LF, Spear R, McCallum H (2009) Impact and dynamics of disease in species threatened by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Conserv Biol 23: 1242-1252.
135. New LF, Matthiopoulos J, Redpath S, Buckland ST (2009) Fitting models of multiple hypotheses to partial population data: investigating the causes of cycles in red grouse. Am Nat 174: 399-412.
136. Newman KB, Buckland ST, Lindley ST, Thomas L, Fernández C (2006) Hidden process models for animal population dynamics. Ecol Appl 16: 74-86.
137. Newman KB, Fernandez C, Thomas L, Buckland ST (2009) Monte Carlo inference for state-space models of wild animal populations. Biometrics 65(2): 572-583.
138. Nichols JD, Hines JE (2002) Approaches for the direct estimation of λ, and demographic contributions to λ, using capture-recapture data. J Appl Stat 29: 539-568.
139. Nichols JD, Hines JE, Lebreton JD, Pradel R (2000) Estimation of contributions to population growth: a reverse-time capture-recapture approach. Ecol Lett 81: 3362-3376.
140. Nichols JD, Hines JE, Mackenzie DI, Seamans ME, Gutierrez RJ (2007) Occupancy estimation and modeling with multiple states and state uncertainty. Ecol Lett 88: 1395-1400.
141. Oli MK, Venkataraman M, Klein PA, Wendland LD, Brown MB (2006) Population dynamics of infectious diseases: a discrete time model. Ecol Model 198: 183-194.
142. Ozgul A, Oli MK, Boker BJ, Perez-Hyedrich C (2009) Upper respiratory tract disease, force of infection, and effects on survival of gopher tortoises. Ecol Appl 19: 786-798.
143. Patterson TA, Thomas L, Wilcox C, Ovaskainen O, Matthiopoulos J (2008) State-space models of individual animal movement. Trends Ecol Evol 23: 87-94.
144. Pledger S, Efford M, Pollock K, Collazo J, Lyons J (2009) Stopover duration analysis with departure probability dependent on unkown time since arrival. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 349-363.
145. Pradel R (1996) Utilization of capture-mark-recapture for the study of recruitment and population growth rate. Biometrics 52: 703-709.
146. Pradel R (2005) Multievent: an extension of multistate capture-recapture models to uncertain states. Biometrics 61: 442-447.
147. Pradel R (2009) The stakes of capture-recapture models with state uncertainty. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 781-795.
148. Pradel R, Maurin-Bernier L, Gimenez O, Genovart M, Choquet R, Oro D (2008) Estimation of sex-specific survival with uncertainty in sex assessment. Can J Stat 36: 29-42.
149. Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. P IEEE 77: 257-286.
150. Ramsey D, Spencer N, Caley P, Efford M, Hansen K, Lam M, Cooper D (2002) The effects of reducing population density on contact rates between brushtail possums: implications for transmission of bovine tuberculosis. J Appl Ecol 39: 806-818.
151. Roberts MG (1996) The dynamics of bovine tuberculosis in possum populations, and its eradication or control by culling or vaccination. J Anim Ecol 64: 451-464.
152. Rosychuk RJ, Islam S (2009) Parameter estimation in a model for misclassified Markov data-a Bayesian approach. Comput Stat Data An 53(11): 3805-3816.
153. Roweis S, Ghahramani Z (1999) A unifying review of linear Gaussian models. Neural Comput Appl 11: 305-345.
154. Royle J, Dorazio R (2008) Hierarchical modeling and inference in ecology. Academic, New York.
155. Royle JA (2008) Modeling individual effects in the Cormack-Jolly-Seber model: a state-space formulation. Biometrics 64: 364-370.
156. Samuel MD, Takekawa JY, Baranyuk VV, Orthmeyer DL (1999) Effects of avian cholera on survival of Lesser Snow Geese Anser caerulescens: an experimental approach. Bird Study 46: 239-247.
157. Schauber EM, Woolf A (2003) Chronic wasting disease in deer and elk: a critique of current models and their application. Wildl Soc B 31: 610-616.
158. Schmidtmann I (2008) Estimating completeness in cancer registries-comparing capture-recapture methods in a simulation study. Biometrical J 50: 1077-1092.
159. Schofield MR, Barker RJ (2008) A unified capture-recapture framework. J Agric Biol Environ S 13: 458-477.
160. Schofield MR, Barker RJ (2009) A further step toward the 'mother-of-all-models': flexilibity and functionality in the modeling of capture-recapture data. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 677-692.
161. Schofield MR, Barker RJ, MacKenzie DI (2009) Flexible hierarchical mark-recapture modeling for open populations using WinBUGS. Environ Ecol Stat 16: 369-387.
162. Schwartz CC, Haroldson MA, White GC, Harris RB, Cherry S, Keating KA, Moody D, Servheen C (2006) Temporal, spatial, and environmental influences on the demographics of grizzly bears in the Greater Yellowstone ecosystem. Wildl Monogr 162: 1-68.
163. Schwarz CJ (2002) Real and quasi-experiments in capture-recapture studies. J Appl Stat 29: 459-473.
164. Schwarz CJ (2009) Migration and movement-the next stage. In: Thomson DL, Cooch EG, Conroy MJ (eds) Modeling demographic processes in marked populations, environmental and ecological statistics series, vol 3. Springer, New York, pp 323-348.
165. Schwarz CJ, Arnason AN (1996) A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52: 860-873.
166. Schwarz CJ, Schweigert JF, Arnason AN (1993) Estimating migration rates using tag-recovery data. Biometrics 49: 177-193.
167. Senar JC, Conroy MJ (2004) Multi-state analysis of the impacts of avian pox on a population of serins (Serinus serinus): the importance of estimating recapture rates. Anim Biodivers Conserv 27: 133-146.
168. Sisson SA, Fan Y, Tanaka MM (2007) Sequential Monte Carlo without likelihoods. Proc Natl Acad Sci USA 104: 1760-1765.
169. Slattery SM, Alisauskas RT (2002) Use of the Barker model in an experiment examining covariate effects on first-year survival in Ross's geese (Chen rossii): a case study. J Appl Stat 29: 497-508.
170. Smith AA (1993) Estimating nonlinear time-series models using simulated vector autoregressions. J Appl Econ 8: S63-S84.
171. Smith GC, Cheeseman CL (2002) A mathematical model for the control of disease in wildlife populations: culling, vaccination and fertility control. Ecol Model 150: 45-53.
172. Smith GC, Cheeseman CL, Clifton-Hadley RS (2001) A model of bovine tuberculosis in the badger Meles meles: an evaluation of control strategies. J Appl Ecol 38: 509-519.
173. Smith T, Vounatsou P (2003) Estimation of infection and recovery rates for highly polymorphic parasites when detectability is imperfect, using hidden Markov models. Stat Med 22: 1709-1724.
174. Streftaris G, Gibson GJ (2004) Bayesian analysis of experimental epidemics of foot-and-mouth disease. Proc R Soc Lond B 271: 1111-1117.
175. Tavecchia G, Besbeas P, Coulson T, Morgan BJT, Clutton-Brock TH (2009) Estimating population size and hidden demographic parameters with state-space modeling. Am Nat 173: 722-733.
176. Telfer S, Bennett M, Bown K, Cavanagh R, Crespin L, Hazel S, Jones T, Begon M (2002) The effects of cowpox virus on survival in natural rodent populations: increases and decreases. J Anim Ecol 71: 558-568.
177. Thomas L, Buckland ST, Newman KB, Harwood J (2005) A unified framework for modelling wildlife population dynamics. Aust NZ J Stat 47: 19-34.
178. Thompson K (2007) Use of site occupancy models to estimate prevalence of of myxobolus cerebralis infection in trout. J Aquat Anim Health 19: 8-13.
179. Titman AC, Sharples LD (2008) A general goodness-of-fit test for Markov and hidden Markov models. Stat Med 27: 2177-2195.
180. Titman AC, Sharples LD (2009) Model diagnostics for multi-state models. Stat Meth Med Res: 1-31, doi: 10. 1177/0962280209105541.
181. Viallefont A, Auget JL (1999) Using capture-recapture models to estimate transition rates between states in interval-censored data. Rev Epidemiol Sante Publ 47: 627-634.
182. van Boven M, Weissing FJ (2004) The evolutionary economics of immunity. Am Nat 163: 277-294.
183. Wang G (2007) On the latent state estimation of nonlinear population dynamics using Bayesian and non-Bayesian state-space models. Ecol Model 200: 521-528.
184. Wasserberg G, Osnas EE, Rolley RE, Samuel MD (2009) Host culling as an adaptive management tool for chronic wasting disease in white-tailed deer: a modelling study. J Appl Ecol 46: 457-466.
185. Webb CT, Brooks CP, Gage KL, Antolin MF (2006) Classic flea-borne transmission does not drive plague epizootics in prairie dogs. Proc Natl Acad Sci USA 103: 6236-6241.
186. Williams BK, Nichols JD, Conroy MJ (2002) Analysis and management of animal populations. Academic, New York.
187. Yip P, Bruno G, Tajima N, Seber G, Buckland S, Cormack R, Unwin N, Chang Y, Fienberg S, Junker B, Laporte R, Libman I, McCarty D (1995) Capture-recapture and multiple-record systems estimation. 1. History and theoretical development. Am J Epidemiol 142: 1047-1058.
188. Yip P, Bruno G, Tajima N, Seber G, Buckland S, Cormack R, Unwin N, Chang Y, Fienberg S, Junker B, Laporte R, Libman I, McCarty D (1995) Capture-recapture and multiple-record systems estimation. 2. Applications in human diseases. Am J Epidemiol 142: 1059-1068.
189. Zucchini W, Raubenheimer D, MacDonald IL (2008) Modeling time series of animal behavior by means of a latent-state model with feedback. Biometrics 64: 807-815.