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@book{alberthu2019,
edition = {1st edition},
title = {Probability and {Bayesian} {Modeling}},
publisher = {{Chapman and Hall/CRC}},
author = {Albert, J. and Hu, J.},
year = {2019},
}
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author = {Arnason, N. A. },
journal = {Researches on Population Ecology},
number = {2},
pages = {97--113},
title = {Parameter estimates from mark-recapture experiments on two populations subject to migration and death},
volume = {13},
year = {1972}}
@article{arnason1973,
author = {Arnason, N. A.},
journal = {Researches on Population Ecology},
number = {2},
pages = {1--8},
title = {The estimation of population size, migration rates and survival in a stratified population},
volume = {15},
year = {1973}}
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author = {Adam, Timo and Griffiths, Christopher A. and Leos-Barajas, Vianey and Meese, Emily N. and Lowe, Christopher G. and Blackwell, Paul G. and Righton, David and Langrock, Roland},
title = {Joint modelling of multi-scale animal movement data using hierarchical hidden {M}arkov models},
journal = {Methods in Ecology and Evolution},
volume={10},
number={9},
pages={1536--1550},
year = {2019},
doi = {10.1111/2041-210X.13241},
}
@article{Altman2007,
title={Mixed hidden {M}arkov models: an extension of the hidden {M}arkov model to the longitudinal data setting},
author={Altman, Rachel MacKay},
journal={Journal of the American Statistical Association},
volume={102},
number={477},
pages={201--210},
year={2007},
publisher={Taylor \& Francis}
}
@article{auger2020introduction,
title={An introduction to state-space modeling of ecological time series},
author={Auger-M{\'e}th{\'e}, Marie and Newman, Ken and Cole, Diana and Empacher, Fanny and Gryba, Rowenna and King, Aaron A and Leos-Barajas, Vianney and Flemming, Joanna Mills and Nielsen, Anders and Petris, Giovanni and others},
journal={arXiv preprint arXiv:2002.02001},
year={2020}
}
@Article{barb99,
author = {Barbraud, C. and Barbraud, J.~C. and Barbraud, M.},
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year = 1999,
volume = 141,
pages = {469-479}
}
@InProceedings{bair91,
author = {Bairlein, F.},
title = {Population studies of white storks ciconia ciconia in Europe, with reference to the western population},
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pages = {207 -- 229},
year = 1991,
editor = {Perrins, C. and Lebreton, J.-D. and Hirons, G.},
publisher = {Oxford: Oxford University Press.}
}
@article{bancila2018te,
author = {B\v{a}ncil\v{a}, R. I. and Pradel, R. and Choquet, R. and Pl\v{a}iasu, R. and Gimenez, O.},
title = {Using temporary emigration to inform movement behaviour of cave-dwelling invertebrates: a case study of a cave harvestman species},
journal = {Ecological Entomology},
volume = {43},
number = {5},
pages = {551-559},
year = {2018}
}
@ARTICLE{Benhaiem2018,
AUTHOR={Benhaiem, S. and Marescot, L. and Hofer, H. and East, M. L. and Lebreton, J.-D. and Kramer-Schadt, S. and Gimenez, O.},
TITLE={Robustness of Eco-Epidemiological Capture-Recapture Parameter Estimates to Variation in Infection State Uncertainty},
JOURNAL={Frontiers in Veterinary Science},
VOLUME={5},
PAGES={197},
YEAR={2018}
}
@article{BesbeasMorgan2019,
title={Exact inference for integrated population modelling},
author={Besbeas, P. and Morgan, B.J.T.},
journal={Biometrics},
volume={75},
number={2},
pages={475--484},
year={2019},
publisher={Wiley Online Library}
}
@book{BegonEtAl2006,
title={Ecology: From Individuals to Ecosystems},
author={Begon, M. and Harper, J.L. and Townsend, C.R.},
edition = {4th edition},
year={2006},
publisher={Wiley-Blackwell}
}
@article{BeisnerEtAl2003,
author = {Beisner, B.E. and Haydon, D.T. and Cuddington, K.},
title = {Alternative stable states in ecology},
journal = {Frontiers in Ecology and the Environment},
volume = {1},
number = {7},
pages = {376-382},
doi = {10.1890/1540-9295(2003)001[0376:ASSIE]2.0.CO;2},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/1540-9295},
year = {2003}
}
@article{BeyerEtAl2013,
title={The effectiveness of {B}ayesian state-space models for estimating behavioural states from movement paths},
author={Beyer, Hawthorne L and Morales, Juan M and Murray, Dennis and Fortin, Marie-Jos{\'e}e},
journal={Methods in Ecology and Evolution},
volume={4},
number={5},
pages={433--441},
year={2013},
publisher={Wiley Online Library}
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author = {Bonner, S. J. and Schwarz, C. J.},
journal = {Biometrics},
number = {1},
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title = {An extension of the {C}ormack--{J}olly--{S}eber model for continuous covariates with application to Microtus pennsylvanicus},
volume = {62},
year = {2006}}
@article{bonner_continuous_2010,
title = {Continuous {Covariates} in {Mark}-{Recapture}-{Recovery} {Analysis}: {A} {Comparison} of {Methods}},
volume = {66},
number = {4},
journal = {Biometrics},
author = {Bonner, S. J. and Morgan, B. J. T. and King, R.},
year = {2010},
pages = {1256--1265}
}
@article{Borchers2008,
title={Spatially explicit maximum likelihood methods for capture--recapture studies},
author={Borchers, David L and Efford, MG},
journal={Biometrics},
volume={64},
number={2},
pages={377--385},
year={2008},
publisher={Wiley Online Library}
}
@article{BorgyEtAl2015,
title={Dynamics of weeds in the soil seed bank: a hidden {M}arkov model to estimate life history traits from standing plant time series},
author={Borgy, Benjamin and Reboud, Xavier and Peyrard, Nathalie and Sabbadin, R{\'e}gis and Gaba, Sabrina},
journal={PLoS ONE},
volume={10},
number={10},
pages={e0139278},
year={2015},
publisher={Public Library of Science}
}
@article{BreiningerEtAl2010,
title={Multistate modeling of habitat dynamics: factors affecting {F}lorida scrub transition probabilities},
author={Breininger, David R and Nichols, James D and Duncan, Brean W and Stolen, Eric D and Carter, Geoffrey M and Hunt, Danny K and Drese, John H},
journal={Ecology},
volume={91},
number={11},
pages={3354--3364},
year={2010},
publisher={Wiley Online Library}
}
@book{BrooksEtAl2011,
title={Handbook of Markov Chain Monte Carlo},
author={Brooks, Steve and Gelman, Andrew and Jones, Galin and Meng, Xiao-Li},
year={2011},
publisher={CRC press}
}
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}
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volume = {31},
year = {2016}}
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volume = {171},
year = {2004},
}
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address = {Switzerland},
author = {Burnham, K. P.},
booktitle = {Marked Individuals in the Study of Bird Populations},
editor = {Lebreton, J. -D. and North, P. M.},
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year = {1993},
}
@book{BurnhamAnderson2002,
author = {Burnham, K. P. and Anderson, D. R.},
publisher = {Springer-Verlag},
title = {Model selection and multimodel inference: {A} practical information-theoretic approach},
year = {2002},
edition = {2nd edition}
}
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author = {Burnham, K. P. and Anderson, D. R. and White, G. C. and Brownie, C. and Pollock, K. H.},
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title = {Design and analysis methods for fish survival experiments based on release-recapture},
volume = {5},
year = {1987},
}
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author = {Burnham, K. P. and Overton, W. S.},
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volume = {60},
year = {1979},
}
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author = {Burnham, K. P. and Rexstad, E. A.},
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volume = {49},
year = {1993},
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author = {Cam, E. and Link, W. A. and Cooch, E. G. and Monnat, J. Y. and Danchin, E.},
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title = {Individual covariation in life-history traits: Seeing the trees despite the forest},
volume = {159},
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}
@book{CappeEtAl2005,
title={Inference in Hidden {M}arkov Models},
author={Capp{\'e}, Olivier and Moulines, Eric and Ryd{\'e}n, Tobias},
year={2005},
publisher={New York: Springer}
}
@book{Caswell2001,
author = {Caswell, H.},
publisher = {Sinauer},
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edition = {2nd edition},
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@article{CayuelaEtAl2020,
title={Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations},
author={Cayuela, Hugo and Besnard, Aur{\'e}lien and Cote, Julien and Laporte, Martin and Bonnaire, Eric and Pichenot, Julian and Schtickzelle, Nicolas and Bellec, Arnaud and Joly, Pierre and L{\'e}na, Jean-Paul},
journal={Ecological Monographs},
publisher={Wiley Online Library},
volume={90},
pages={e01406},
year={2020},
}
@article{ChambertEtAl2012,
title={Exposure of black-legged kittiwakes to {L}yme disease spirochetes: dynamics of the immune status of adult hosts and effects on their survival},
author={Chambert, Thierry and Staszewski, Vincent and Lobato, Elisa and Choquet, R{\'e}mi and Carrie, C{\'e}cile and McCoy, Karen D and Tveraa, Torkild and Boulinier, Thierry},
journal={Journal of Animal Ecology},
volume={81},
number={5},
pages={986--995},
year={2012},
publisher={Wiley Online Library}
}
@article{chambert2014,
author = {Chambert, T. and Rotella, J. J. and Higgs, M. D.},
journal = {Ecology and Evolution},
number = {8},
pages = {1389-1397},
title = {Use of posterior predictive checks as an inferential tool for investigating individual heterogeneity in animal population vital rates},
volume = {4},
year = {2014}}
@article{ChenEtAl2013,
title={Imperfect detection is the rule rather than the exception in plant distribution studies},
author={Chen, Guoke and K{\'e}ry, Marc and Plattner, Matthias and Ma, Keping and Gardner, Beth},
journal={Journal of Ecology},
volume={101},
number={1},
pages={183--191},
year={2013},
publisher={Wiley Online Library}
}
@incollection{ChoquetEtAl2009,
title={Program {E}-{SURGE}: a software application for fitting multievent models},
author={Choquet, R. and Rouan, L. and Pradel, R.},
booktitle={Modeling demographic processes in marked populations},
editor = {Thomson, D. L. and Cooch, E. G. and Conroy, M. J.},
pages={845-865},
year={2009},
publisher={Springer}
}
@article{ChoquetEtAl2011,
title={A semi-{M}arkov model to assess reliably survival patterns from birth to death in free--ranging populations},
author={Choquet, R. and Viallefont, A. and Rouan, L. and Gaanoun, K. and Gaillard, J.-M.},
journal={Methods in Ecology and Evolution},
volume={2},
number={4},
pages={383--389},
year={2011}
}
@article{ChoquetEtAl2017,
title={Transient state estimation using continuous-time processes applied to opportunistic capture--recapture data},
author={Choquet, R{\'e}mi and Garnier, Alexandre and Awuve, Edem and Besnard, Aur{\'e}lien},
journal={Ecological Modelling},
volume={361},
pages={157--163},
year={2017},
publisher={Elsevier}
}
@article{choquet2014stopover,
author = {Choquet, R. and B{\'e}chet, A. and Gu{\'e}don, Y.},
journal = {Ecology and Evolution},
title = {Applications of hidden hybrid Markov/semi-Markov models: from stopover duration to breeding success dynamics},
volume = {4},
year = {2014}}
@article{choquet2013stopover,
author = {Choquet, R. and Guédon, Y. and Besnard, Y. and Guillemain, M. and Pradel, R.},
journal = {Ecological Modelling},
title = {Estimating stop over duration in the presence of trap-effects},
volume = {250},
number = {10},
pages = {111--118},
year = {2013}}
@book{cole2020,
title={Parameter Redundancy and Identifiability},
author={Cole, D.},
year={2020},
publisher={{Chapman and Hall/CRC}}
}
@Article{Cole2019,
author="Cole, Diana J.",
title="Parameter redundancy and identifiability in hidden {M}arkov models",
journal="METRON",
year="2019",
volume="77",
number="2",
pages="105--118"
}
@article{choquet2018modulated,
author = {Choquet, R.},
title = {{M}arkov-modulated {P}oisson processes as a new framework for analysing capture--recapture data},
journal = {Methods in Ecology and Evolution},
volume = {9},
number = {4},
pages = {929-935},
year = {2018}
}
@article{cook1967expectancy,
title={The Accuracy of a Population Estimation from Multiple Recapture Data},
author={Cook, L.M.M and Brower, L. P. and Croze, H. J.},
journal={Journal of Animal Ecology},
volume={36},
number={1},
pages={57--60},
year={1967},
publisher={Wiley Online Library}
}
@article{cooch2012disease,
title={Disease dynamics in wild populations: modeling and estimation: a review},
author={Cooch, E.G. and Conn, P.B. and Ellner, S.P. and Dobson, A.P. and Pollock, K.H.},
journal={Journal of Ornithology},
volume={152},
number={2},
pages={485--509},
year={2012}
}
@article{ConnCooch2009,
title={Multistate capture--recapture analysis under imperfect state observation: {A}n application to disease models},
author={Conn, P.B. and Cooch, E.G.},
journal={Journal of Applied Ecology},
volume={46},
number={2},
pages={486--492},
year={2009}
}
@article{cubaynes2012,
author = {Cubaynes, S. and Lavergne, C. and Marboutin, E. and Gimenez, O.},
title = {Assessing individual heterogeneity using model selection criteria: how many mixture components in capture--recapture models?},
journal = {Methods in Ecology and Evolution},
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