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@article{alldredge_etal:2007,
  title={Time-of-detection method for estimating abundance from point-count surveys},
  author={Alldredge, M.W. and Pollock, K.H. and Simons, T.R. and Collazo, J.A. and Shriner, S.A. and Johnson, DH},
  journal={The Auk},
  volume={124},
  number={2},
  pages={653--664},
  year={2007},
  publisher={BioOne}
}


@book{buckland_distsamp_2001,
	author = {S. T. Buckland and D. R. Anderson and K. P. Burnham and J. L. Laake and D. L. Borchers and L. Thomas},
	title = {Introduction to distance sampling -- Estimating abundance of biological populations},
	publisher = {Oxford University Press},
	year = {2001}
}


@article{chandler_etal:2009,
  title={Scrub-shrub bird habitat associations at multiple spatial scales in beaver meadows in Massachusetts},
  author={Chandler, R.B. and King, D.I. and DeStefano, S.},
  journal={The Auk},
  pages={186--197},
  year={2009},
  publisher={JSTOR}
}

@article{chandlerEA_2011,
	title = {Inference about density and temporary emigration in unmarked populations},
	volume = {92},
	number = {7},
	journal = {Ecology},
	author = {R. B. Chandler and J. A. Royle and D. I. King},
	month = jul,
	year = {2011},
	pages = {1429--1435}
}




@article{dorazio_etal:2005,
	title = {Improving {removal-based} Estimates of Abundance by Sampling a Population of Spatially Distinct Subpopulations},
	volume = {61},
	number = {4},
	journal = {Biometrics},
	author = {Robert M. Dorazio and Howard L. Jelks and Frank Jordan},
	year = {2005},
	pages = {1093--1101}
}



@article{efford:2004,
author = {Efford, M},
journal = {Oikos},
number = {3},
pages = {598--610},
publisher = {Blackwell Synergy},
title = {{Density estimation in live-trapping studies}},
volume = {106},
year = {2004}
}


@Article{fiskeChandler_2011,
   author        = {Ian Fiske and Richard Chandler},
   title         = {\textbf{unmarked}: An {\textbf{R}} Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance},
   journal       = {Journal of Statistical Software},
   year          = {2011},
   volume        = {43},
   number        = {10},
   pages         = {1--23},
   url           = {http://www.jstatsoft.org/v43/i10/}
}




@Manual{hijmans_vanEtten:2012,
       title = {raster: Geographic analysis and modeling with raster data},
       author = {Robert J. Hijmans & Jacob van Etten},
       year = {2012},
       note = {R package version 1.9-67},
       url = {http://CRAN.R-project.org/package=raster},
       }




@article{kendall_etal:1997,
	title = {Estimating temporary emigration using {capture-recapture} data with {P}ollock{'}s robust design},
	volume = {78},
	number = {2},
	journal = {Ecology},
	author = {William L. Kendall and James D. Nichols and James E. Hines},
	year = {1997},
	pages = {563--578}
},



@article{kery_modeling_2005,
	title = {Modeling avian abundance from replicated counts using binomial mixture models},
	volume = {15},
	number = {4},
	journal = {Ecological Applications},
	author = {M. Kery and J. A. Royle and H. Schmid},
	year = {2005},
	pages = {1450--1461}
},





@article{link:2003,
  title={Nonidentifiability of Population Size from Capture-Recapture Data with Heterogeneous Detection Probabilities},
  author={Link, W.A.},
  journal={Biometrics},
  volume={59},
  number={4},
  pages={1123--1130},
  year={2003}
}





@article{mackenzie_estimating_2002,
	title = {Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One},
	volume = {83},
	number = {8},
	journal = {Ecology},
	author = {Darryl I. {MacKenzie} and James D. Nichols and G. B. Lachman and S. Droege and J. A. Royle and C. A. Langtimm},
	year = {2002},
	keywords = {occupancy, unmarked},
	pages = {2248--2255}
}

@article{Tyre_2002,
  author = {Tyre, A.J. and Tenhumberg, B. and Field, S.A. and Niejalke, D. and Parris, K.,
and Possingham, H.P.},
  year = {2003},
  title = {Improving precision and reducing bias in biological surveys: estimating false-negative error rates},
  journal = {Ecological Applications},
  volume = {13},
  pages = {1790-1801}
}





@article{mackenzie_estimating_2003,
	title = {Estimating Site Occupancy, Colonization, and Local Extinction When a Species is Detected Imperfectly},
	volume = {84},
	number = {8},
	journal = {Ecology},
	author = {Darryl I. {MacKenzie} and James D. Nichols and James E. Hines and Melinda G. Knutson and Alan B. Franklin},
	year = {2003},
	keywords = {colonization, occupancy},
	pages = {2200--2207}
}






@article{nichols_double-observer_2000,
	author = {James D. Nichols and James E. Hines and John R. Sauer and Frederick W. Fallon and Jane E. Fallon and Patricia J. Heglund},
	title = {A {Double-Observer} Approach for Estimating Detection Probability and Abundance from Point Counts},
	volume = {117},
	number = {2},
	journal = {The Auk},
	year = {2000},
	pages = {393--408}
},



@article{otis_etal:1978,
  title={Statistical inference from capture data on closed animal populations},
  author={Otis, D.L. and Burnham, K.P. and White, G.C. and Anderson, D.R.},
  journal={Wildlife monographs},
  number={62},
  pages={3--135},
  year={1978},
}





@article{royle_general_2005,
	title = {A General Class of Multinomial Mixture Models for Anuran Calling Survey Data},
	volume = {86},
	number = {9},
	journal = {Ecology},
	author = {J. A. Royle and W. A. Link},
	year = {2005},
	pages = {2505--2512}
},



@article{royle_modeling_2004,
	title = {Modeling abundance effects in distance sampling},
	volume = {85},
	number = {6},
	journal = {Ecology},
	author = {J. A. Royle and D. K. Dawson and S. Bates},
	year = {2004},
	keywords = {distance},
	pages = {1591--1597}
},




@article{royle_estimating_2003,
	title = {Estimating abundance from repeated presence-absence data or point counts},
	volume = {84},
	number = {3},
	journal = {Ecology},
	author = {J. A. Royle and J. D. Nichols},
	year = {2003},
	keywords = {unmarked},
	pages = {777--790}
},






@article{royle_young:2008,
annote = {From Duplicate 1 ( A Hierarchical Model For Spatial Capture-Recapture Data - Royle, J A; Young, K V )

},
author = {Royle, J A and Young, K V},
journal = {Ecology},
number = {8},
pages = {2281--2289},
title = {{A Hierarchical Model For Spatial Capture-Recapture Data}},
volume = {89},
year = {2008}
}


@article{royle_n-mixture_2004,
	title = {N-mixture models for estimating population size from spatially replicated counts},
	volume = {60},
	number = {1},
	journal = {Biometrics},
	author = {J. A Royle},
	year = {2004},
	pages = {108--115}
},




@book{royle_dorazio:2008,
  title={Hierarchical modeling and inference in ecology: the analysis of data from populations, metapopulations and communities},
  author={Royle, J.A. and Dorazio, R.M.},
  year={2008},
  publisher={Academic Press}
}




@article{royle_generalized_2004,
	title = {Generalized estimators of avian abundance from count survey data},
	volume = {27},
	number = {1},
	journal = {Animal Biodiversity and Conservation},
	author = {J. A. Royle},
	year = {2004},
	pages = {375--386}
},


@Book{sarkar:2008,
    title = {Lattice: Multivariate Data Visualization with R},
    author = {Deepayan Sarkar},
    publisher = {Springer},
    address = {New York},
    year = {2008},
    note = {ISBN 978-0-387-75968-5},
    url = {http://lmdvr.r-forge.r-project.org},
  }




@article{schmid_etal:2004,
         author={Schmid, H. and Zbinden, N. and Keller, V.},
         year={2004},
         title={\"{U}berwachung der Bestandsentwicklung h\"{a}ufiger Brutv\"{o}gel in der Schweiz},
         journal={Swiss Ornithological Institute Sempach Switzerland}
}




@article{sillett_etal:2012,
  title={Hierarchical distance sampling models to estimate population size and habitat-specific abundance of an island endemic},
  author={Sillett, S. and Chandler, R.B. and Royle, J.A. and K{\'e}ry, M. and Morrison, S.A.},
  journal={Ecological Applications},
  volume={22},
  pages={1997-2006},
  year={2012},
  publisher={Eco Soc America}
}



@book{williams_etal:2002,
author = {Williams, B K and Nichols, J D and Conroy, M J},
publisher = {Academic Pr},
title = {{Analysis and management of animal populations: modeling, estimation, and decision making}},
year = {2002}
}

@article{Guillera_2012,
author = {Guillera-Arroita, Gurutzeta and Lahoz-Monfort, José J.},
title = {Designing studies to detect differences in species occupancy: power analysis under imperfect detection},
journal = {Methods in Ecology and Evolution},
volume = {3},
number = {5},
pages = {860-869},
keywords = {hypothesis testing, likelihood-ratio test, multiple-season occupancy, sample size, survey design, Wald test},
doi = {https://doi.org/10.1111/j.2041-210X.2012.00225.x},
url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2012.00225.x},
year = {2012}
}

@article{Amundson_2014,
    author = {Amundson, Courtney L. and Royle, J. Andrew and Handel, Colleen M.},
    title = "{A hierarchical model combining distance sampling and time removal to estimate detection probability during avian point counts}",
    journal = {The Auk},
    volume = {131},
    number = {4},
    pages = {476-494},
    year = {2014},
    month = {07},
    issn = {1938-4254},
    doi = {10.1642/AUK-14-11.1},
    url = {https://doi.org/10.1642/AUK-14-11.1},
    eprint = {https://academic.oup.com/auk/article-pdf/131/4/476/26883760/auk0476.pdf},
}


@article{Rota2016,
 author = {Rota, Christopher T. and Ferreira, Marco A. R. and Kays, Roland and Forrester, Tavis D. and Kalies, Elizabeth L. and McShea, William J. and Parsons, Arielle W. and Millspaugh, Joshua J.},
 title = {A multi-species occupancy model for two or more interacting species},
 journal = {Methods in Ecology and Evolution},
 year = {2016},
 url = {http://dx.doi.org/10.1111/2041-210X.12587},
 doi = {10.1111/2041-210X.12587},
 volume = {7},
 pages = {1164-1173},
}

@article{Clipp_2021,
 author = {Clipp, Hannah L. and Evans, Amber L. and Kessinger, Brin E. and Kellner, Kenneth and Rota, Christopher T.},
 title = {A penalized likelihood for multispecies occupancy models improves predictions of species interactions},
 journal = {Ecology},
 year = {2021},
 pages = {e03520},
 addendum = {\href{https://doi.org/10.1002/ecy.3520}{[view]}}
}

@book{Kery_2010,
  author = {K\'{e}ry, Marc},
  title = {{Introduction to WinBUGS for Ecologists}},
  year = {2010},
  publisher={Academic Press}
}

@article{Hanski_1998,
  author = {Hanski, I},
  title = {Metapopulation dynamics},
  year = {1998},
  journal = {Nature},
  volume = {396},
  pages = {41-49}
}

@book{Kery_2011,
  author = {K\'{e}ry, Marc and Schaub, Michael},
  title = {{Bayesian Population Analysis using WinBUGS: A Hierarchical Perspective}},
  year = {2011},
  publisher = {Academic Press}
}

@book{McCullagh_1989,
  author = {McCullagh, P and Nelder, J. A.},
  year = {1989},
  title = {Generalized linear models},
  publisher = {Chapman and Hall}
}

@article{Kery_2008,
  author = {K\'{e}ry, M., and Schmidt, B.R},
  year = {2008},
  title = {Imperfect detection and its consequences for monitoring for conservation},
  journal = {Community Ecology},
  volume = {9},
  pages = {207-2016}
}

@article{Royle_2007,
  author = {Royle, J.A.,and K\'{e}ry, M.},
  year = {2007},
  title = {A {B}ayesian state-space formulation of dynamic occupancy models},
  journal = {Ecology},
  volume = {88},
  pages = {1813-1823}
}

@article{Moilanen_2002,
  author = {Moilanen, A.},
  year = {2002},
  title = {Implications of empirical data quality to metapopulation model parameter estimation and application},
  journal = {Oikos},
  volume = {96},
  pages = {516-530}
}

@article{Weir_2009, 
  author = {Weir, L., I.J. Fiske, and J.A. Royle},
  year = {2009},
  title = {Trends in anuran occupancy from northeastern states of the {N}orth {A}merican {A}mphibian {M}onitoring {P}rogram},
  journal = {Herpetological Conservation and Biology},
  volume = {4},
  pages = {389-402}
}

@book{Davison_1997,
  author = {Davison, A.C and Hinkley, D.V.},
  year = {1997},
  title = {Bootstrap Methods and Their Application},
  publisher = {Cambridge University Press}
}

@article{Hosmer_1997, 
  author = {Hosmer, D.W. and Hosmer, T. and le Cressie, S. and Lemeshow, S.},
  year = {1997},
  title = {A comparision of goodness-of-fit tests for the logistic regression model},
  journal = {Statistics in Medicine},
  volume = {16},
  pages = {965-980}
}

@article{MacKenzie_2004,
  author = {MacKenzie, D.I and Bailey, L.},
  year = {2004},
  title = {Assessing the fit of site-occupancy models},
  journal = {Journal of Agricultural, Biological, and Environmental Statistics},
  volume = {9},
  pages = {300-318}
}