This will hopefully grow to a comprehensive resources reference to anyone who is thinking of entering the realm of SECR. Some paper may not be explicitly mark-recapture oriented, but are closely knit with the methods.
Royle, J. A., Chandler, R. B., Sollmann, R., Gardner, B. (2013). Spatial mark-recapture. Academic press (ISBN: 9780124059399) (Bookdepository)
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Augustine, B. and Royle, A. (2016) SPIM: Open population SCR MCMC sampler. R package available on GitHub
Cox, M. J., Borcher, D. L., Kelly, N., Borchers, D. L., & Kelly, N. (2013). nupoint: An R package for density estimation from point transects in the presence of nonuniform animal density. Methods in Ecology and Evolution, 4(6), 1–18. http://doi.org/10.1111/2041-210X.12058
Efford, M. G., Dawson, D. K., & Robbins, C. S. (2004). DENSITY: Software for analysing capture-recapture data from passive detector arrays. Animal Biodiversity and Conservation, 27(1), 217–228. http://doi.org/1
Efford, M. G. (2015). secr: Spatially explicit capture-recapture models. R package version 2.10.0. http://CRAN.R-project.org/package=secr
Efford, M. G. (2017). What could possibly go wrong? Troubleshooting spatially explicit capture–recapture models in secr 3.0. http://www.otago.ac.nz/density/pdfs/secr-troubleshooting.pdf
Efford, M. G. (2017). A tutorial on fitting spatially explicit capture–recapture models in secr. http://www.otago.ac.nz/density/pdfs/secr-tutorial.pdf
Fiske, I., Chandler, R. (2011). unmarked: An R Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance. Journal of Statistical Software, 43(10), 1-23. URL http://www.jstatsoft.org/v43/i10/
Gopalaswamy, A. M., Royle, J. A., Hines, J. E., Singh, P., Jathanna, D., Kumar, N. S., & Karanth, K. U. (2012). Program SPACECAP: Software for estimating animal density using spatially explicit capture-recapture models. Methods in Ecology and Evolution, 3(6), 1067–1072. http://doi.org/10.1111/j.2041-210X.2012.00241.x
Ivan, J. S., & Newkirk, E. S. (2016). Cpw Photo Warehouse: A custom database to facilitate archiving, identifying, summarizing and managing photo data collected from camera traps. Methods in Ecology and Evolution, 7(4), 499–504. http://doi.org/10.1111/2041-210X.12503
Laake, J.L. (2013). RMark: An R Interface for Analysis of Capture-Recapture Data with MARK. AFSC Processed Rep 2013-01, 25p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand Point Way NE, Seattle WA 98115
McClintock, B. T. (2015). Multimark: An R package for analysis of capture-recapture data consisting of multiple “noninvasive” marks. Ecology and Evolution, 5(21), 4920–4931. http://doi.org/10.1002/ece3.1676
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Muscarella, R., Galante, P. J., Soley-Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., & Anderson, R. P. (2014). ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5(11), 1198–1205. http://doi.org/10.1111/2041-210X.12261
Nguyen, T., Sinha, A., Gholami, S., Plumptre, A. J., Joppa, L. N., Tambe, M., … Beale, C. M. (2016). CAPTURE: A New Predictive Anti-Poaching Tool for Wildlife Protection. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (AAMAS).
Niedballa, J., Sollmann, R., Courtiol, A., & Wilting, A. (2016). camtrapR: an R package for efficient camera trap data management. Methods in Ecology and Evolution. http://doi.org/10.1111/2041-210X.12600
Royle, J. A., Chandler, R. B., Sollman, R., Gardner, B. (2013). scrbook R package. https://sites.google.com/site/spatialcapturerecapture/scrbook-r-package
Royle, J. A., Karanth, K. U., Gopalaswamy, A. M., Kumar, N. S. (2009). SCRbayes R package. https://sites.google.com/site/spatialcapturerecapture/scrbayes-r-package
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Distiller, G., & Borchers, D. L. (2015). A spatially explicit capture-recapture estimator for single-catch traps. Ecology and Evolution, 5(21), 5075–5087. http://doi.org/10.1002/ece3.1748
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