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@article{Bates_2015,
author = {Bates, Douglas and Mächler, Martin and Bolker, Ben and Walker, Steve},
title = {Fitting Linear Mixed-Effects Models Using lme4},
journal = {Journal of Statistical Software},
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number = {1},
volume = {67},
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}
@article{Carpenter_2017,
author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matthew D. and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus and Guo, Jiqiang and Li, Peter and Riddell, Allen},
title = {Stan: A Probabilistic Programming Language},
journal = {Journal of Statistical Software},
publisher = {Foundation for Open Access Statistic},
year = {2017},
number = {1},
volume = {76},
url = {http://dx.doi.org/10.18637/jss.v076.i01},
doi = {10.18637/jss.v076.i01}
}
@article{Chandler2011,
author = {Chandler, Richard B. and Royle, J. Andrew and King, David I.},
title = {Inference about density and temporary emigration in unmarked populations},
journal = {Ecology},
year = {2011},
number = {7},
volume = {92},
pages = {1429--1435},
url = {http://dx.doi.org/10.1890/10-2433.1},
doi = {10.1890/10-2433.1},
file = {:Chandler2011b.pdf:PDF},
keyword = {Chestnut-sided Warbler, Dendroica pensylvanica, N-mixture model, USA, White Mountain National Forest, detection probability, hierarchical, models, population density, spot-mapping, temporary emigration, unmarked populations}
}
@article{Fiske_2011,
author = {Fiske, Ian and Chandler, Richard and others, },
title = {Unmarked: an {R} package for fitting hierarchical models of wildlife occurrence and abundance},
journal = {Journal of Statistical Software},
year = {2011},
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pages = {1--23},
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}
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author = {Gelman, Andrew and Hill, Jennifer},
title = {Data analysis using regression and multilevel/hierarchical models},
publisher = {Cambridge University Press},
year = {2007},
pages = {651},
url = {http://dx.doi.org/10.2277/0521867061, http://dx.doi.org/10.2277/0521867061},
doi = {10.2277/0521867061},
address = {New York, NY},
file = {:Gelman2007.pdf:PDF},
isbn = {0521867061},
pmid = {14341096}
}
@article{Hoffman_2014,
author = {Hoffman, Matthew D and Gelman, Andrew},
title = {The {N}o-{U}-{T}urn sampler: adaptively setting path lengths in {H}amiltonian {M}onte {C}arlo.},
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year = {2014},
number = {1},
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}
@article{MacKenzie_2002,
author = {MacKenzie, Darryl I. and Nichols, James D. and Lachman, Gideon B. and Droege, Sam and Royle, J. Andrew and Langtimm, Catherine A.},
title = {Estimating site occupancy rates when detection probabilities are less than one},
journal = {Ecology},
publisher = {Wiley},
year = {2002},
month = {aug},
number = {8},
volume = {83},
pages = {2248--2255},
url = {http://dx.doi.org/10.1890/0012-9658(2002)083[2248:esorwd]2.0.co;2},
doi = {10.1890/0012-9658(2002)083[2248:esorwd]2.0.co;2}
}
@article{MacKenzie_2004a,
author = {MacKenzie, Darryl I. and Bailey, Larissa L.},
title = {Assessing the fit of site-occupancy models},
journal = {Journal of Agricultural, Biological, and Environmental Statistics},
year = {2004},
number = {3},
volume = {9},
pages = {300--318},
doi = {10.1198/108571104x3361}
}
@article{Schmid_2004,
author = {Schmid, Hans and Zbinden, Niklaus and Keller, Verena},
title = {Überwachung der bestandsentwicklung häufiger brutvögel in der schweiz},
journal = {Swiss Ornithological Institute Sempach Switzerland},
year = {2004}
}
@article{Vehtari_2017,
author = {Vehtari, Aki and Gelman, Andrew and Gabry, Jonah},
title = {Practical {B}ayesian model evaluation using leave-one-out cross-validation and {WAIC}},
journal = {Statistics and Computing},
year = {2017},
number = {5},
volume = {27},
pages = {1413--1432},
doi = {10.1007/s11222-016-9696-4}
}
@article{Wright_2019,
author = {Wright, Wilson J. and Irvine, Kathryn M. and Higgs, Megan D.},
title = {Identifying occupancy model inadequacies: can residuals separately assess detection and presence?},
journal = {Ecology},
year = {2019},
pages = {e02703},
doi = {10.1002/ecy.2703}
}
@article{Yackulic_2020,
author = {Yackulic, Charles B. and Dodrill, Michael and Dzul, Maria and Sanderlin, Jamie S. and Reid, Janice A.},
title = {A need for speed in {B}ayesian population models: a practical guide to marginalizing and recovering discrete latent states},
journal = {Ecological Applications},
year = {2020},
number = {5},
volume = {30},
doi = {10.1002/eap.2112}
}
@article{Broms_2014,
author = {Broms, Kristin M. and Johnson, Devin S. and Altwegg, Res and Conquest, Loveday L.},
title = {Spatial occupancy models applied to atlas data show Southern Ground Hornbills strongly depend on protected areas},
journal = {Ecological Applications},
volume = {24},
number = {2},
pages = {363-374},
doi = {https://doi.org/10.1890/12-2151.1},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-2151.1},
year = {2014}
}
@article{Clark_2019,
author = {Clark, Allan E. and Altwegg, Res},
title = {Efficient Bayesian analysis of occupancy models with logit link functions},
journal = {Ecology and Evolution},
volume = {9},
number = {2},
pages = {756-768},
doi = {https://doi.org/10.1002/ece3.4850},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4850},
year = {2019}
}
@article{Hodges_2010,
title={Adding spatially-correlated errors can mess up the fixed effect you love},
author={Hodges, James S and Reich, Brian J},
journal={The American Statistician},
volume={64},
number={4},
pages={325--334},
year={2010},
publisher={Taylor \& Francis}
}
@article{Johnson_2013,
author = {Johnson, Devin S. and Conn, Paul B. and Hooten, Mevin B. and Ray, Justina C. and Pond, Bruce A.},
title = {Spatial occupancy models for large data sets},
journal = {Ecology},
volume = {94},
number = {4},
pages = {801-808},
doi = {https://doi.org/10.1890/12-0564.1},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-0564.1},
year = {2013}
}
@book{Banerjee_2014,
title={Hierarchical modeling and analysis for spatial data},
author={Banerjee, Sudipto and Carlin, Bradley P and Gelfand, Alan E},
year={2014},
publisher={CRC press}
}
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