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SECRbook.bib
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@Article{be08,
author = {Borchers, D. L. and Efford, M. G.},
journal = {Biometrics},
title = {Spatially explicit maximum likelihood methods for capture-recapture studies},
year = {2008},
pages = {377-385},
volume = {64},
doi = {10.1111/j.1541-0420.2007.00927.x},
file = {:D\:/Admin/MGE papers/Borchers and Efford 2008 Biometrics.pdf:PDF},
}
@Article{density2012,
author = {Efford, M. G.},
title = {DENSITY 5.0: software for spatially explicit capture-recapture},
year = {2012},
note = {Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand},
file = {:D\:/Density 5.0/bin5/Density5.chm:CHM},
url = {https://www.otago.ac.nz/density},
}
@Article{lbca92,
author = {Lebreton, J.-D. and Burnham, K. P. and Clobert, J. and Anderson, D. R.},
journal = {Ecological Monographs},
title = {Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies},
year = {1992},
pages = {67-118},
volume = {62},
file = {:D\:/Papers/Lebreton-EcoMonog-1992.pdf:PDF},
}
@Article{obwa78,
author = {Otis, D. L. and Burnham, K. P. and White, G. C. and Anderson, D. R.},
journal = {Wildlife Monographs},
title = {Statistical inference from capture data on closed animal populations},
year = {1978},
number = {62},
file = {:D\:/Papers/Otis et al 1978.pdf:PDF},
}
@Manual{R-base,
title = {R: A Language and Environment for Statistical
Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2024},
url = {https://www.R-project.org/},
}
@Manual{R-secr,
title = {{secr: Spatially explicit capture-recapture models}},
author = {Efford, M. G.},
note = {R package version 4.6.6},
year = {2025},
keywords = {R package},
url = {https://CRAN.R-project.org/package=secr},
}
@Book{bk2014,
author = {Borchers, D. L. and Kidney, D.},
publisher = {University of St Andrews},
title = {Flexible density surface estimation for spatially explicit capture--recapture surveys},
year = {2014},
number = {2014-1},
series = {CREEM Technical Report},
url = {https://research-repository.st-andrews.ac.uk/bitstream/handle/10023/9147/secrgam_techrep.pdf?sequence=1},
}
@Article{bvns02,
author = {Boyce, M. S. and Vernier, P. R. and Nielsen, S. E. and Schmiegelow, F. K. A.},
journal = {Ecological modelling},
title = {Evaluating resource selection functions},
year = {2002},
pages = {281-300},
volume = {157},
file = {:D\:/Papers/Boyce et al 2002 Ecological_Modelling RSF.pdf:PDF},
}
@Article{em14,
author = {Efford, M. G. and Mowat, G.},
journal = {Ecology},
title = {Compensatory heterogeneity in spatially explicit capture-recapture data},
year = {2014},
pages = {1341-1348},
volume = {95},
file = {:D\:/Admin/MGE papers/Efford and Mowat 2014 Ecology.pdf:PDF},
}
@Article{j80,
author = {Johnson, D. H.},
journal = {Ecology},
title = {The comparison of usage and availability measurements for evaluating resource preference},
year = {1980},
pages = {65-71},
volume = {61},
file = {:D\:/Papers/Johnson 1980 Ecology habitat use.pdf:PDF},
}
@Article{p2000,
author = {Pledger, S.},
journal = {Biometrics},
title = {Unified maximum likelihood estimates for closed capture-recapture models using mixtures},
year = {2000},
pages = {434-442},
volume = {56},
file = {:D\:/Papers/Pledger 2000.pdf:PDF},
}
@Book{w06,
author = {Wood, S. N.},
publisher = {Chapman and Hall/CRC},
title = {Generalized Additive Models: An Introduction with {R}},
year = {2006},
}
@Article{drns21,
author = {Dupont, G. and Royle, J. A. and Nawaz, M. A. and Sutherland, C.},
journal = {Ecology},
title = {Optimal sampling design for spatial capture-recapture},
year = {2021},
pages = {e03262},
volume = {102},
file = {:D\:/Density communication/Design/References/Dupont et al 2021 Ecology SECR design.pdf:PDF},
keywords = {design},
}
@Article{dbss21,
author = {Durbach, I. and Borchers, D. and Sutherland, C. and Sharma, K.},
journal = {Methods in Ecology and Evolution},
title = {Fast, flexible alternatives to regular grid designs for spatial capture-recapture},
year = {2021},
number = {298-310},
pages = {2041-210},
volume = {12},
doi = {10.1111/2041-210X.13517},
file = {:D\:/Density communication/Design/References/Durbach et al 2021 MEE design.pdf:PDF},
keywords = {design},
}
@InCollection{ebb09,
author = {Efford, M. G. and Borchers, D. L. and Byrom, A. E.},
booktitle = {Modeling Demographic Processes in Marked Populations},
publisher = {Springer},
title = {Density estimation by spatially explicit capture-recapture: likelihood-based methods},
year = {2009},
address = {New York.},
editor = {D. L. Thomson and E. G. Cooch and M. J. Conroy},
pages = {255-269},
file = {:D\:/Admin/MGE papers/Efford Borchers and Byrom 2009.pdf:PDF},
}
@Article{eb19,
author = {Efford, M. G. and Boulanger, J.},
journal = {Methods in Ecology and Evolution},
title = {Fast evaluation of study designs for spatially explicit capture-recapture},
year = {2019},
pages = {1529-1535},
volume = {10},
doi = {10.1111/2041-210X.13239},
file = {:D\:/Admin/MGE papers/Efford and Boulanger 2019 MEE fast evaluation.pdf:PDF},
keywords = {design},
}
@Article{w15,
author = {Wolters, M. A.},
journal = {Journal of Statistical Software, Code Snippets},
title = {A genetic algorithm for selection of fixed-size subsets with application to design problems},
year = {2015},
pages = {1-18},
volume = {68},
doi = {10.18637/jss.v068.c01},
file = {:D\:/Density communication/Design/References/Wolters 2015 kofnGA.pdf:PDF},
}
@Article{edjq16,
author = {Efford, M. G. and Dawson, D. K. and Jhala, Y. V. and Qureshi, Q.},
journal = {Ecography},
title = {Density-dependent home-range size revealed by spatially explicit capture-recapture},
year = {2016},
pages = {676-688},
volume = {39},
file = {:D\:/Admin/MGE papers/Efford Dawson Jhala and Qureshi 2016 ECOGRAPHY_E01511.pdf:PDF},
}
@Article{h89,
author = {Huggins, R. M.},
journal = {Biometrika},
title = {On the statistical analysis of capture experiments},
year = {1989},
pages = {133-140},
volume = {76},
file = {:D\:/Papers/huggins 1989.pdf:PDF},
}
@book{s82,
address = {London},
author = {Seber, G. A. F.},
edition = {2nd},
publisher = {Griffin},
title = {The estimation of animal abundance and related parameters.},
year = {1982},
}
@Book{cw,
editor = {Cooch, E. and White, G},
title = {Program MARK: A Gentle Introduction.},
year = {2023},
edition = {23rd},
file = {:D\:/Papers/mark_book.pdf:PDF},
url = {http://www.phidot.org/software/mark/docs/book/},
}
@Article{edb09,
author = {Efford, M. G. and Dawson, D. K. and Borchers, D. L.},
journal = {Ecology},
title = {Population density estimated from locations of individuals on a passive detector array},
year = {2009},
pages = {2676-2682},
volume = {90},
file = {:D\:/Admin/MGE papers/Efford Dawson & Borchers 2009 Ecology with appendices.pdf:PDF},
}
@Article{ef13,
author = {Efford, M. G. and Fewster, R. M.},
journal = {Oikos},
title = {Estimating population size by spatially explicit capture-recapture},
year = {2013},
pages = {918-928},
volume = {122},
file = {:D\:/Admin/MGE papers/Efford and Fewster 2013 Oikos.pdf:PDF},
}
@incollection{fb04,
address = {Oxford, U. K.},
author = {Fewster, R. M. and Buckland, S. T.},
booktitle = {Advanced distance sampling},
editor = {S. T. Buckland and D. R. Anderson and K. P. Burnham and J. L. Laake and D. L. Borchers and L. Thomas},
pages = {281-306},
publisher = {Oxford University Press},
title = {Assessment of distance sampling estimators},
year = {2004},
}
@book{wnc02,
address = {San Diego},
author = {Williams, B. K. and Nichols, J. D. and Conroy, M. J.},
publisher = {Academic Press},
title = {Analysis and management of animal populations},
year = {2002},
}
@Article{e04,
author = {Efford, M. G.},
journal = {Oikos},
title = {Density estimation in live-trapping studies},
year = {2004},
pages = {598-610},
volume = {106},
file = {:D\:/Admin/MGE papers/Efford 2004 Oikos.pdf:PDF},
keywords = {SECR general},
}
@Article{ebm13,
author = {Efford, M. G. and Borchers, D. L. and Mowat, G.},
journal = {Methods in Ecology and Evolution},
title = {Varying effort in capture-recapture studies},
year = {2013},
pages = {629-636},
volume = {4},
file = {:D\:/Admin/MGE papers/Efford Borchers and Mowat 2013 MEE.pdf:PDF},
}
@Book{rcsg14,
author = {Royle, J. A. and Chandler, R. B. and Sollmann, R. and Gardner, B.},
publisher = {Academic Press},
title = {Spatial capture-recapture},
year = {2014},
keywords = {SECR general},
}
@Article{cc58,
author = {Calhoun, J. B. and Casby, J. U.},
journal = {Public Health Monograph},
title = {Calculation of home range and density of small mammals},
year = {1958},
number = {55},
publisher = {U.S. Government Printing Office},
}
@Manual{R-secrlinear,
title = {{secrlinear: Spatially Explicit Capture-Recapture for Linear Habitats}},
author = {Efford, M. G.},
note = {R package version 1.2.2},
year = {2024},
keywords = {R package},
url = {https://CRAN.R-project.org/package=secrlinear},
}
@InCollection{ec04,
author = {Efford, M. G. and Cowan, P. E.},
booktitle = {The Biology of Australian Possums and Gliders},
publisher = {Surrey Beatty \& Sons},
title = {Long-term population trend of \emph{Trichosurus {v}ulpecula} in the Orongorongo Valley, New Zealand},
year = {2004},
address = {Chipping Norton},
editor = {R. L. Goldingay and S. M. Jackson},
pages = {471-483},
file = {:D\:/Admin/MGE papers/Efford and Cowan 2004.pdf:PDF},
}
@Article{f11,
author = {Fewster, R. M.},
journal = {Biometrics},
title = {Variance estimation for systematic designs in spatial surveys},
year = {2011},
pages = {1518-1531},
volume = {67},
file = {:D\:/Papers/Fewster 2011 Biometrics variance estimation systematic designs.pdf:PDF},
}
@manual{R-raster,
author = {Hijmans, R. J.},
journal = {R package version 3.6-26},
title = {raster: Geographic Data Analysis and Modeling},
year = {2023},
url = {https://CRAN.R-project.org/package=raster},
}
@Article{pb05,
author = {Pebesma, E. J. and Bivand, R. S.},
journal = {R News},
title = {Classes and methods for spatial data in R},
year = {2005},
volume = {5},
keywords = {R package},
url = {https://cran.r-project.org/doc/Rnews/},
}
@Article{ry08,
author = {Royle, J. A. and Young, K. V.},
journal = {Ecology},
title = {A hierarchical model for spatial capture-recapture data},
year = {2008},
pages = {2281-2289},
volume = {89},
file = {:D\:/Density communication/Applications of SECR/Royle and Young 2008.pdf:PDF},
}
@InCollection{w78,
author = {Ward, G. D.},
booktitle = {The ecology of arboreal folivores},
publisher = {Smithsonian Institute Press},
title = {Habitat use and home range of radio-tagged opossums \emph{Trichosurus {v}ulpecula} (Kerr) in New Zealand lowland forest},
year = {1978},
address = {Washington D.C.},
editor = {G. G. Montgomery},
pages = {267-287},
}
@article{de09,
author = {Dawson, D. K. and Efford, M. G.},
journal = {Journal of Applied Ecology},
pages = {1201-1209},
title = {Bird population density estimated from acoustic signals},
volume = {46},
year = {2009},
}
@article{edr04,
author = {Efford, M. G. and Dawson, D. K. and Robbins, C. S.},
journal = {Animal Biodiversity and Conservation},
pages = {217-228},
title = {DENSITY: software for analysing capture-recapture data from passive detector arrays},
volume = {27},
year = {2004},
}
@book{estmw,
author = {Efford, M. G. and Spencer, N. J. and Thomas, B. W. and Mason, R. F. and Williams, P.},
publisher = {in prep},
title = {Distribution of sympatric skink species in relation to habitat},
}
@Article{stmd98,
author = {Spencer, N. J. and Thomas, B. W. and Mason, R. F. and Dugdale, J. S.},
journal = {New Zealand Journal of Zoology},
title = {Diet and life history variation in the sympatric lizards \emph{Oligosoma {n}igriplantare {p}olychroma} and \emph{Oligosoma {l}ineoocellatum}},
year = {1998},
pages = {457-463},
volume = {25},
}
@Article{ewcb05,
author = {Efford, M. G. and Warburton, B. and Coleman, M. C. and Barker, R. J.},
journal = {Wildlife Society Bulletin},
title = {A field test of two methods for density estimation},
year = {2005},
pages = {731-738},
volume = {33},
file = {:D\:/Admin/MGE papers/Efford et al WSB 2005.pdf:PDF},
}
@article{sdr60,
author = {Stamm, D. D. and Davis, D. E. and Robbins, C. S.},
journal = {Bird-Banding},
pages = {115-130},
title = {A method of studying wild bird populations by mist-netting and banding},
volume = {31},
year = {1960},
}
@Article{Stephens2000,
author = {Stephens, M.},
journal = {Journal of the Royal Statistical Society Series B},
title = {Dealing with label switching in mixture models},
year = {2000},
pages = {795-809},
volume = {62},
}
@Article{cr13,
author = {Chandler, R. B. and Royle, J. A.},
journal = {Annals of Applied Statistics},
title = {Spatially explicit models for inference about density in unmarked or partially marked populations},
year = {2013},
pages = {936-954},
volume = {7},
file = {:D\:/Density communication/Applications of SECR/Chandler and Royle 2013.pdf:PDF},
}
@Article{eh18,
author = {Efford, M. G. and Hunter, C. M.},
journal = {Biometrics},
title = {Spatial capture-mark-resight estimation of animal population density},
year = {2018},
pages = {411-420},
volume = {74},
doi = {10.1111/biom.12766},
file = {:D\:/Admin/MGE papers/Efford and Hunter 2017 Biometrics.pdf:PDF},
}
@article{mmpcl13,
author = {Matechou, E. and Morgan, B. J. T. and Pledger, S. and Collazo, J. A. and Lyons, J. E.},
journal = {Journal of Agricultural, Biological and Environmental Statistics},
pages = {120-135},
title = {Integrated analysis of capture-recapture-resighting data and counts of unmarked birds at stopover sites},
volume = {18},
year = {2013},
}
@Article{mw12,
author = {McClintock, B. T. and White, G. C.},
journal = {Journal of Ornithology, Supplement 2},
title = {From NOREMARK to MARK: software for estimating demographic parameters using mark-resight methodology},
year = {2012},
pages = {S641-S650},
volume = {152},
file = {:D\:/Papers/McClintock and White 2012 JO mark-resight.pdf:PDF},
}
@Article{rksnmapdbed14,
author = {Rich, L. N. and Kelly, M. J. and Sollmann, R. and Noss, A. J. and Maffei, L. and Arispe, R. L. and Paviolo, A. and De Angelo, C. D. and Di Blanco and Y. E. and Di Bitetti, M. S.},
journal = {Journal of Mammalogy},
title = {Comparing capture-recapture, mark-resight, and spatial mark-resight models for estimating puma densities via camera traps},
year = {2014},
pages = {382-391},
volume = {95},
file = {:D\:/Density communication/Applications of SECR/Rich et al 2014 J Mamm SECR mark-resight.pdf:PDF},
keywords = {mark-resight},
}
@article{rswmd15,
author = {Rutledge, M. E. and Sollmann, R. and Washburn, B. E. and Moorman, C. E. and DePerno, C. S.},
journal = {Wildlife Research},
pages = {447-453},
title = {Using novel spatial mark-resight techniques to monitor resident Canada geese in a suburban environment},
volume = {41},
year = {2015},
}
@Article{sgpsmspo13,
author = {Sollmann, R. and Gardner, B. and Parsons, A. W. and Stocking, J. J. and McClintock, B. T. and Simons, T. R. and Pollock, K. H. and O'Connell, A. F.},
journal = {Ecology},
title = {A spatial mark-resight model augmented with telemetry data},
year = {2013},
pages = {553-559},
volume = {94},
file = {:D\:/Density communication/Applications of SECR/Sollmann et al 2013 A SMR model augmented with telemetry data..pdf:PDF},
}
@Article{whc18,
author = {Whittington, J. and Hebblewhite, M. and Chandler, R.},
journal = {Journal of Applied Ecology},
title = {Generalized spatial mark-resight models with an application to grizzly bears},
year = {2018},
pages = {157-168},
volume = {55},
file = {:D\:/Density communication/Applications of SECR/Whittington_et_al-2018-Journal_of_Applied_Ecology.pdf:PDF},
}
@article{hb83,
author = {Hayes, R. J. and Buckland, S. T.},
journal = {Biometrics},
pages = {29-42},
title = {Radial-distance models for the line-transect method},
volume = {39},
year = {1983},
}
@incollection{lr08,
author = {Laake, J. and Rexstad, E.},
booktitle = {Program MARK. A Gentle Introduction. 6th edition.},
editor = {Cooch and E. and White, G.},
title = {Appendix C. RMark - an alternative approach to building linear models in MARK},
year = {2008},
url = {http://www.phidot.org},
}
@Article{rmgvl11,
author = {Royle, J. A. and Magoun, A. J. and Gardner, B. and Valkenburg, P. and Lowell, R. E.},
journal = {Journal of Wildlife Management},
title = {Density estimation in a wolverine population using spatial capture-recapture models},
year = {2011},
pages = {604-611},
volume = {75},
file = {:D\:/Density communication/Applications of SECR/Royle et al 2011 JWM wolverines.pdf:PDF},
}
@book{vr99,
author = {Venables, W. N. and Ripley, B. D.},
edition = {3rd},
publisher = {Springer},
title = {Modern Applied Statistics with S-Plus},
year = {1999},
}
@article{cn06,
author = {Csardi, G. and Nepusz, T.},
journal = {InterJournal},
title = {The igraph software package for complex network research},
volume = {1695},
year = {2006},
url = {http://igraph.org},
}
@Article{e14,
author = {Efford, M. G.},
journal = {Methods in Ecology and Evolution},
title = {Bias from heterogeneous usage of space in spatially explicit capture-recapture analyses},
year = {2014},
pages = {599-602},
volume = {5},
file = {:D\:/Admin/MGE papers/Efford 2014 MEE bias from heterogeneous usage of space.pdf:PDF},
}
@article{ms00,
author = {Mowat, G. and Strobeck, C.},
journal = {Journal of Wildlife Management},
pages = {183-193},
title = {Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis},
volume = {64},
year = {2000},
}
@Article{rcgg13,
author = {Royle, J. A. and Chandler, R. B. and Gazenski, K. D. and Graves, T. A.},
journal = {Ecology},
title = {Spatial capture-recapture models for jointly estimating population density and landscape connectivity},
year = {2013},
pages = {287-294},
volume = {94},
file = {:D\:/Density communication/Applications of SECR/Royle et al 2013 Ecology landscape connectivity.pdf:PDF},
}
@Article{sfr15,
author = {Sutherland, C. and Fuller, A. K. and Royle, J. A.},
journal = {Methods in Ecology and Evolution},
title = {Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks},
year = {2015},
pages = {169-177},
volume = {6},
file = {:D\:/Density communication/Applications of SECR/Sutherland_et_al-2015-Methods_in_Ecology_and_Evolution.pdf:PDF},
}
@Manual{R-gdistance,
title = {gdistance: distances and routes on geographical grids},
author = {{van Etten}, J.},
note = {R package version 1.6.4},
year = {2023},
url = {https://CRAN.R-project.org/package=gdistance},
}
@Article{grw09,
author = {Gardner, B. and Royle, J. A. and Wegan, M. T.},
journal = {Ecology},
title = {Hierarchical models for estimating density from DNA mark-recapture studies},
year = {2009},
pages = {1106-1115},
volume = {90},
file = {:D\:/Density communication/Applications of SECR/Gardner et al 2009.pdf:PDF},
}
@article{d13,
author = {Dorazio, R. M.},
journal = {PLoS ONE},
pages = {e84017},
title = {Bayes and empirical Bayes estimators of abundance and density from spatial capture-recapture data},
volume = {8},
year = {2013},
}
@Article{e11,
author = {Efford, M. G.},
journal = {Ecology},
title = {Estimation of population density by spatially explicit capture-recapture analysis of data from area searches},
year = {2011},
pages = {2202-2207},
volume = {92},
file = {:D\:/Admin/MGE papers/Efford 2011 Ecology.pdf:PDF},
}
@Article{mtr11,
author = {Marques, T. A. and Thomas, L. and Royle, J. A.},
journal = {Ecology},
title = {A hierarchical model for spatial capture-recapture data: Comment},
year = {2011},
pages = {526-528},
volume = {92},
file = {:D\:/Papers/Marques et al 2011 Ecology 10-1440.pdf:PDF},
}
@Manual{R-RcppNumerical,
author = {Qiu, Y. and Balan, S. and Beall, M. and Sauder, M. and Okazaki, N. and Hahn, T.},
title = {RcppNumerical: 'Rcpp' Integration for Numerical Computing Libraries},
note = {R package version 0.6-0},
year = {2023},
url = {https://CRAN.R-project.org/package=RcppNumerical},
}
@article{cskmh99,
author = {Clark, J. S and Silman, M. and Kern, R. and Macklin, E. and HilleRisLambers, J.},
journal = {Ecology},
pages = {1475-1494},
title = {Seed dispersal near and far: patterns across temperate and tropical forests},
volume = {80},
year = {1999},
}
@book{cws10,
address = {Ithaca, New York},
author = {Charif, R. A. and Waack, A. M. and Strickman, L. M.},
publisher = {Cornell Laboratory of Ornithology},
title = {Raven Pro 1.4 User's Manual},
year = {2010},
}
@Article{sbasgm15,
author = {Stevenson, B. C. and Borchers, D. L. and Altwegg, R. and Swift, R. J. and Gillespie, D. M. and Measey, G. J.},
journal = {Methods in Ecology and Evolution},
title = {A general framework for animal density estimation from acoustic detections across a fixed microphone array},
year = {2015},
pages = {38-48},
volume = {6},
file = {:D\:/Density communication/Applications of SECR/Stevenson et al 2015 MEE acoustic mee312291.pdf:PDF},
}
@Manual{R-spsurvey,
title = {spsurvey: Spatial Sampling Design and Analysis},
author = {Dumelle, M. and Kincaid, T. M. and Olsen, A. R. and Weber, M. H.},
year = {2024},
journal = {R package version 5.5.1},
keywords = {spatial balance},
url = {https://CRAN.R-project.org/package=spsurvey},
}
@article{p18,
author = {Pebesma, E.},
journal = {The R Journal},
number = {1},
pages = {439-446},
title = {Simple features for R: standardized support for spatial vector data},
volume = {10},
year = {2018},
url = {https://doi.org/10.32614/RJ-2018-009},
}
@techreport{p22,
author = {Pebesma, E.},
title = {stars: Spatiotemporal Arrays Raster and Vector Data Cubes},
year = {2022},
url = {https://github.com/r-spatial/stars/, https://r-spatial.github.io/stars/},
}
@Article{bsd99,
author = {Brus, D. J. and Sp\.atjens, L. E. E. M. and de Gruijter, J. J.},
journal = {Geoderma},
title = {A sampling scheme for estimating the mean extractable phosphorus concentration of fields for environmental regulation},
year = {1999},
pages = {129-148},
volume = {89},
file = {:D\:/Density communication/Design/References/Brus and de Gruijter 1997 Geoderma.pdf:PDF},
}
@book{bablbt01,
address = {Oxford},
author = {Buckland, S. T. and Anderson, D. R. and Burnham, K. P. and Laake, J. L. and Borchers, D. L. and Thomas, L.},
publisher = {Oxford University Press},
title = {Introduction to Distance Sampling},
year = {2001},
}
@Article{c19,
author = {Clark, J. D.},
journal = {Population Ecology},
title = {Comparing clustered sampling designs for spatially explicit estimation of population density},
year = {2019},
pages = {93-101},
volume = {61},
file = {:D\:/Density communication/Design/References/Clark 2019 Population Ecology.pdf:PDF},
keywords = {design},
}
@book{c77,
address = {New York, USA},
author = {Cochran, W. G.},
edition = {3rd},
publisher = {John Wiley and Sons},
title = {Sampling Techniques.},
year = {1977},
}
@article{crbjrf08,
author = {Conroy, M. J. and Runge, J. P. and Barker, R. and J., Schofield and M. R. and Fonnesbeck, C. J.},
journal = {Ecology},
pages = {3362-3370},
title = {Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling},
volume = {89},
year = {2008},
}
@book{dbbk06,
address = {Springer},
author = {de Gruijter, J. J. and Brus, D. J. and Bierkens, M. F. P. and Knotters, M.},
publisher = {New York},
title = {Sampling for Natural Resource Monitoring},
year = {2006},
}
@article{es87,
author = {Eberhardt, L. L. and Simmons, M. A.},
journal = {Journal of Wildlife Management},
pages = {665-675},
title = {Calibrating population indices by double sampling},
volume = {51},
year = {1987},
}
@article{fsb16,
author = {Fewster, R. M. and Stevenson, B. C. and Borchers, D. L.},
journal = {Statistical Science},
pages = {245-258},
title = {Trace-contrast models for capture-recapture without capture histories},
volume = {31},
year = {2016},
}
@article{rcr15,
author = {Ramsey, D. S. L. and Caley, P. A. and Robley, A.},
journal = {Journal of Wildlife Management},
pages = {491-499},
title = {Estimating population density from presence–absence data using a spatially explicit model},
volume = {79},
year = {2015},
}
@Article{es20,
author = {Efford, M. G. and Schofield, M. R.},
journal = {Biometrics},
title = {A spatial open-population capture-recapture model},
year = {2020},
pages = {392-402},
volume = {76},
file = {:D\:/Admin/MGE papers/Efford and Schofield 2020 Biometrics spatial open population capture-recapture.pdf:PDF},
}
@book{be07,
author = {Borchers, D. L. and Efford, M. G.},
title = {Supplements to Biometrics paper},
year = {2007},
url = {https://www.otago.ac.nz/density},
}
@article{gvccm04,
author = {Gimenez, O. and Viallefont, A. and Catchpole, E. A. and Choquet, R. and Morgan, B. J. T.},
journal = {Animal Biodiversity and Conservation},
pages = {561-572},
title = {Methods for investigating parameter redundancy},
volume = {27},
year = {2004},
}
@Article{lc24,
author = {Laake, J. L. and Collier, B. A.},
journal = {Journal of Wildlife Management},
title = {Understanding implications of detection heterogeneity in wildlife abundance estimation},
year = {2024},
pages = {e22516},
volume = {88},
doi = {10.1002/jwmg.22516},
file = {:D\:/Density communication/Applications of SECR/Laake and Collier 2023 JWM Understanding implications of detection heterogeneity in wildlife abundance estimation.pdf:PDF},
}
@Manual{SPACECAP,
title = {A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models},
author = {A. M. Gopalaswamy and J. A. Royle and M. E. Meredith and P. Singh and D. Jathanna and N. S. Kumar and K. U. Karanth},
year = {2014},
note = {R package version 1.1.0},
}
@Article{srl19,
author = {Sutherland, C. and J. A. Royle and D. W. Linden},
journal = {Ecography},
title = {oSCR: a spatial capture-recapture {R} package for inference about spatial ecological processes},
year = {2019},
pages = {1459--1469},
volume = {42},
doi = {10.1111/ecog.04551},
file = {:D\:/Density communication/Applications of SECR/Sutherland_et_al-2019-Ecography.pdf:PDF},
}
@Article{Turek2021,
author = {Turek, D. and Milleret, C. and Ergon, T. and Brøseth, H. and Dupont, P. and Bischof, R. and de Valpine, P.},
journal = {Ecosphere},
title = {Efficient estimation of large‐scale spatial capture–recapture models},
year = {2021},
issn = {2150-8925},
month = feb,
number = {2},
volume = {12},
doi = {10.1002/ecs2.3385},
file = {:D\:/Density communication/Applications of SECR/Turek et al 2021 ecs2.3385.pdf:PDF},
publisher = {Wiley},
}
@Article{bf16,
author = {Borchers, D. L. and Fewster, R.},
journal = {Statistical Science},
title = {Spatial capture–recapture models},
year = {2016},
issn = {0883-4237},
month = may,
number = {2},
volume = {31},
doi = {10.1214/16-sts557},
file = {:D\:/Density communication/Applications of SECR/Borchers and Fewster 2016 Statistical science.pdf:PDF},
groups = {SECR},
publisher = {Institute of Mathematical Statistics},
}
@Article{Zhang2022,
author = {Zhang, Wei and Chipperfield, Joseph D. and Illian, Janine B. and Dupont, Pierre and Milleret, Cyril and de Valpine, Perry and Bischof, Richard},
journal = {Ecology},
title = {A flexible and efficient Bayesian implementation of point process models for spatial capture–recapture data},
year = {2022},
issn = {1939-9170},
month = nov,
number = {1},
volume = {104},
doi = {10.1002/ecy.3887},
file = {:D\:/Density communication/Applications of SECR/Zhang et al. 2022 Ecology A flexible and efficient Bayesian implementation of point process models for spatial capture.pdf:PDF},
publisher = {Wiley},
}
@Article{Efford2023,
author = {Efford, M. G.},
journal = {Methods in Ecology and Evolution},
title = {{ipsecr: An R package for awkward spatial capture–recapture data}},
year = {2023},
issn = {2041-210X},
month = mar,
number = {5},
pages = {1182--1189},
volume = {14},
doi = {10.1111/2041-210x.14088},
file = {:D\:/Admin/MGE papers/Efford 2023 MEE ipsecr with supplements.zip:zip},
publisher = {Wiley},
}
@Book{illian08,
author = {Illian, J. and A. Penttinen and H. Stoyan and D. Stoyan},
publisher = {Wiley},
title = {Statistical Analysis and Modelling of Spatial Point Patterns},
year = {2008},
address = {Chichester, UK},
isbn = {9780470014912},
}
@Article{Distiller2015,
author = {Distiller, G. and Borchers, D. L.},
journal = {Ecology and Evolution},
title = {A spatially explicit capture–recapture estimator for single‐catch traps},
year = {2015},
issn = {2045-7758},
month = oct,
number = {21},
pages = {5075--5087},
volume = {5},
doi = {10.1002/ece3.1748},
publisher = {Wiley},
}
@Article{Sollmann2024,
author = {Sollmann, Rahel},
journal = {Peer Community Journal},
title = {Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy models},
year = {2024},
issn = {2804-3871},
month = jan,
volume = {4},
doi = {10.24072/pcjournal.357},
file = {:D\:/Density communication/Applications of SECR/Sollmann 2024 10_24072_pcjournal_357.pdf:PDF},
publisher = {Peer Community In},
}
@Manual{R-akima,
title = {{a}kima: Interpolation of Irregularly and Regularly Spaced Data},
author = {Hiroshi Akima and Albrecht Gebhardt},
note = {R package version 0.6-3.4},
year = {2022},
url = {https://CRAN.R-project.org/package=akima},
}
@Manual{R-ipsecr,
title = {ipsecr: Spatially explicit capture-recapture using inverse prediction},
author = {Murray Efford},
note = {R package version 1.4.1},
year = {2024},
keywords = {R package},
url = {https://CRAN.R-project.org/package=ipsecr},
}
@Manual{R-RcppParallel,
title = {RcppParallel: Parallel Programming Tools for 'Rcpp'},
author = {JJ Allaire and Romain Francois and Kevin Ushey and Gregory Vandenbrouck and Marcus Geelnard and {Intel}},
year = {2023},
note = {R package version 5.1.7},
url = {https://CRAN.R-project.org/package=RcppParallel},
}
@Book{Borchers2002,
author = {Borchers, D. L. and Buckland, S. T. and Zucchini, W.},
publisher = {Springer London},
title = {Estimating Animal Abundance},
year = {2002},
isbn = {9781447137085},
doi = {10.1007/978-1-4471-3708-5},
issn = {1431-8776},
journal = {Statistics for Biology and Health},
}
@Manual{R-Rcpp,
title = {Rcpp: Seamless R and C++ Integration},
author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Inaki Ucar and Douglas Bates and John Chambers},
note = {R package version 1.0.11},
year = {2023},
keywords = {R package},
url = {https://CRAN.R-project.org/package=Rcpp},
}
@Article{ef11,
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
journal = {Journal of Statistical Software},
title = {{Rcpp}: Seamless {R} and {C++} Integration},
year = {2011},
number = {8},
pages = {1--18},
volume = {40},
doi = {10.18637/jss.v040.i08},
keywords = {R package},
}
@Book{onk2011,
editor = {O'Connell, A. F. and Nichols, J. D. and Karanth, K. U.},
publisher = {Springer Japan},
title = {Camera Traps in Animal Ecology},
year = {2011},
isbn = {9784431994954},
doi = {10.1007/978-4-431-99495-4},
}
@InCollection{rg11,
author = {Royle, J. A. and Gardner, B.},
booktitle = {Camera traps in animal ecology: Methods and analyses},
publisher = {Springer},
title = {Hierarchical spatial capture-recapture models for estimating density from trapping arrays},
year = {2011},
address = {Tokyo, Japan},