{"id":18404645,"url":"https://github.com/romunov/secr_resources","last_synced_at":"2026-01-22T07:02:51.031Z","repository":{"id":144877593,"uuid":"58264109","full_name":"romunov/secr_resources","owner":"romunov","description":"Resources that might come handy to anyone using spatially explicit mark-capture-recapture models.","archived":false,"fork":false,"pushed_at":"2019-06-15T18:17:49.000Z","size":535,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-12T20:47:19.038Z","etag":null,"topics":["capture-recapture-models","density-estimation","ecology","hierarchical-models","population-density","population-size","spatially-explicit-models"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/romunov.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-05-07T12:01:04.000Z","updated_at":"2025-03-17T11:24:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"aadd3b55-cc1e-4d6c-bb5b-1d6c8585c4a7","html_url":"https://github.com/romunov/secr_resources","commit_stats":{"total_commits":75,"total_committers":2,"mean_commits":37.5,"dds":"0.013333333333333308","last_synced_commit":"11c1ef4de75c59f79a6011f6b40441eb94269b38"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/romunov/secr_resources","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/romunov%2Fsecr_resources","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/romunov%2Fsecr_resources/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/romunov%2Fsecr_resources/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/romunov%2Fsecr_resources/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/romunov","download_url":"https://codeload.github.com/romunov/secr_resources/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/romunov%2Fsecr_resources/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28657549,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["capture-recapture-models","density-estimation","ecology","hierarchical-models","population-density","population-size","spatially-explicit-models"],"created_at":"2024-11-06T02:53:28.666Z","updated_at":"2026-01-22T07:02:51.016Z","avatar_url":"https://github.com/romunov.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"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.\n\n# Books\nRoyle, J. A., Chandler, R. B., Sollmann, R., Gardner, B. (2013). **Spatial mark-recapture**. Academic press (ISBN: 9780124059399) ([Bookdepository](http://www.bookdepository.com/Spatial-Capture-Recapture-J-Andrew-Royle-Richard-B-Chandler-Rahel-Sollmann-Beth-Gardner/9780124059399?ref=grid-view))\n\nWilliams, B., Nichols, J., \u0026 Conroy, M. (2002). **Analysis and management of animal populations. Modeling, estimation, and decision making**. Academic press. Retrieved from http://www.elsevier.com/books/analysis-and-management-of-animal-populations/williams/978-0-12-754406-9\n\n# (R) resources\nAugustine, B. and Royle, A. (2016) **SPIM: Open population SCR MCMC sampler**. [R package available on GitHub](https://github.com/benaug/SPIM)\n\nCox, M. J., Borcher, D. L., Kelly, N., Borchers, D. L., \u0026 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\n\nEfford, M. G., Dawson, D. K., \u0026 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\n\nEfford, M. G. (2015). **secr: Spatially explicit capture-recapture models**. R package version 2.10.0. http://CRAN.R-project.org/package=secr\n\nEfford, M. G. (2017). **What could possibly go wrong? Troubleshooting\nspatially explicit capture–recapture models in secr 3.0.** http://www.otago.ac.nz/density/pdfs/secr-troubleshooting.pdf\n\nEfford, M. G. (2017). **A tutorial on fitting spatially explicit capture–recapture models in secr.** http://www.otago.ac.nz/density/pdfs/secr-tutorial.pdf\n\nFiske, 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/\n\nGopalaswamy, A. M., Royle, J. A., Hines, J. E., Singh, P., Jathanna, D., Kumar, N. S., \u0026 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\n\nIvan, J. S., \u0026 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\n\nLaake, 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\n\nMcClintock, 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\n\nMorin, D., Fuller, A. K., Royle, J. A., \u0026 Sutherland, C. (2017). **Model-based estimators of density and connectivity to inform conservation of spatially structured populations**. Ecosphere, 8(1)(January), 1–16. http://doi.org/10.1002/ecs2.1623\n\nMoya, Ó., Mansilla, P.-L., Madrazo, S., Igual, J.-M., Rotger, A., Romano, A., \u0026 Tavecchia, G. (2015). **APHIS: A new software for photo-matching in ecological studies**. Ecological Informatics, 27, 64–70. http://doi.org/10.1016/j.ecoinf.2015.03.003\n\nMuscarella, R., Galante, P. J., Soley-Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., \u0026 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\n\nNguyen, 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).\n\nNiedballa, J., Sollmann, R., Courtiol, A., \u0026 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\n\nRoyle, J. A., Chandler, R. B., Sollman, R., Gardner, B. (2013). **scrbook R package**. https://sites.google.com/site/spatialcapturerecapture/scrbook-r-package\n\nRoyle, J. A., Karanth, K. U., Gopalaswamy,  A. M., Kumar, N. S. (2009). **SCRbayes R package**. https://sites.google.com/site/spatialcapturerecapture/scrbayes-r-package\n\nSwinnen, K. R. R., Reijniers, J., Breno, M., \u0026 Leirs, H. (2014). **A novel method to reduce time investment when processing videos from camera trap studies**. PloS One, 9(2), e98881. http://doi.org/10.1371/journal.pone.0098881\n\n# Papers\n## Methodological\n\nAugustine, B. C., Royle, J. A., Kelly, M. J., Satter, C. B., Alonso, R. S., \u0026 Crooks, K. R. (2016). **Spatial capture-recapture with partial identity: An application to camera traps**. bioRxiv. http://doi.org/10.1101/056804 ([code](https://github.com/benaug/SCRRcpp))\n\nMoqanaki, E. M., Jiménez, J., \u0026 López-Bao, J. V. (2018). **Counting bears in the Iranian Caucasus : Remarkable mismatch between scientifically-sound population estimates and perceptions**. Biological Cons\n\nBenhamou, S. (1988). **Analyzing spatial relationships from trapping data. Journal of Mammalogy**, 69(4), 828–831. [http://doi.org/10.2307/1381641](http://doi.org/10.2307/1381641)\n\nBoulanger, J., \u0026 McLellan, B. (2001). **Corrigendum: Closure violation in DNA-based mark-recapture estimation of grizzly bear populations**. Canadian Journal of Zoology, 79(8), 1532. [http://doi.org/10.1139/z01-121](http://doi.org/10.1139/z01-121)\n\nBorchers, D. L., \u0026 Efford, M. G. (2008). **Spatially explicit maximum likelihood methods for capture-recapture studies**. Biometrics, 64(2), 377–385. http://doi.org/j.1541-0420.2007.00927.x\n\nBorchers, D. (2012). **A non-technical overview of spatially explicit capture-recapture models**. Journal of Ornithology. http://doi.org/10.1007/s10336-010-0583-z\n\nBorchers, D. L., \u0026 Fewster, R. M. (2013). **Spatial capture-recapture models**. Statistical Science, 1–20. http://doi.org/10.1016/B978-0-12-405939-9.00020-7\n\nBorchers, D., Distiller, G., Foster, R., Harmsen, B., \u0026 Milazzo, L. (2014). **Continuous-time spatially explicit capture-recapture models, with an application to a jaguar camera-trap survey**. Methods in Ecology and Evolution, 5(7), 656–665. http://doi.org/10.1111/2041-210X.12196\n\nBorchers, D. L., Stevenson, B. C., Kidney, D., Thomas, L., \u0026 Marques, T. A. (2015). **A Unifying Model for Capture–Recapture and Distance Sampling Surveys of Wildlife Populations**. Journal of the American Statistical Association, 110(509), 195–204. http://doi.org/10.1080/01621459.2014.893884\n\nBorchers, D. L., \u0026 Marques, T. A. (2017). **From distance sampling to spatial capture–recapture**. AStA Advances in Statistical Analysis. http://doi.org/10.1007/s10182-016-0287-7\n\nBozarth, C. A., Gardner, B., Rockwood, L. L., \u0026 Jesús, E. (2015). **Using fecal DNA and spatial capture-recapture to characterize a recent coyote colonization**. Northeastern Naturalist, 22(1), 144–162. http://doi.org/10.1656/045.022.0124\n\nChandler, R. B., Royle, J. A., \u0026 King, D. I. (2011). **Inference about density and temporary emigration in unmarked populations**. Ecology, 92(7)(7), 1429–1435. http://doi.org/10.1890/10-2433.1\n\nChandler, R. B., \u0026 Andrew Royle, J. (2013). **Spatially explicit models for inference about density in unmarked or partially marked populations**. Annals of Applied Statistics, 7(2), 936–954. http://doi.org/10.1214/12-AOAS610\n\nChandler, R. B., \u0026 Clark, J. D. (2014). **Spatially explicit integrated population models**. Methods in Ecology and Evolution, 5(12), 1351–1360. http://doi.org/10.1111/2041-210X.12153\n\nChandler, R. B., Hepinstall-Cymerman, J., Merker, S., Abernathy-Conners, H., \u0026 Cooper, R. J. (2018). **Characterizing spatio-temporal variation in survival and recruitment with integrated population models**. The Auk, 135(3), 409–426. http://doi.org/10.1642/AUK-17-181.1\n\nCrimmins, S. M., Walleser, L. R., Hertel, D. R., McKann, P. C., Rohweder, J. J., \u0026 Thogmartin, W. E. (2015). **Relating mesocarnivore relative abundance to anthropogenic land-use with a hierarchical spatial count model**. Ecography, (May), n/a–n/a. http://doi.org/10.1111/ecog.01179\n\nDavidson, G. A., Clark, D. A., Johnson, B. K., Waits, L. P., \u0026 Adams, J. R. (2014). **Estimating cougar densities in northeast Oregon using conservation detection dogs**. The Journal of Wildlife Management, 78(6), 1104–1114. http://doi.org/10.1002/jwmg.758\n\nDey, S., Delampady, M., Karanth, K. U., \u0026 Gopalaswamy, A. M. (2017). **A spatially explicit capture recapture model for partially identified individuals when trap detection rate is less than one**. Biometrics, 0, 1–25. Retrieved from https://arxiv.org/pdf/1712.10035.pdf\n\nDistiller, G., \u0026 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\n\nDrewry, J. M., Van Manen, F. T., \u0026 Ruth, D. M. (2013). **Density and genetic structure of black bears in coastal South Carolina**. Journal of Wildlife Management, 77(1), 153–164. http://doi.org/10.1002/jwmg.443\n\nDorazio, R. M. (2013). **Bayes and empirical bayes estimators of abundance and density from spatial capture-recapture data**. PLoS ONE, 8(12), 1–12. http://doi.org/10.1371/journal.pone.0084017\n\nDorazio, R. M. (2014). **Accounting for imperfect detection and survey bias in statistical analysis of presence-only data**. Global Ecology and Biogeography, n/a–n/a. http://doi.org/10.1111/geb.12216\n\nDorazio, R. M. (2016). **Bayesian data analysis in population ecology: motivations, methods, and benefits**. Population Ecology, 58(1), 31–44. http://doi.org/10.1007/s10144-015-0503-4\n\nDutta, T., Sharma, S., Maldonado, J. E., Wood, T. C., Panwar, H. S., \u0026 Seidensticker, J. (2013). **Fine-scale population genetic structure in a wide-ranging carnivore, the leopard (Panthera pardus fusca) in central India**. Diversity and Distributions, 19(7), 760–771. http://doi.org/10.1111/ddi.12024\n\nEfford, M. (2004). **Density estimation in live-trapping studies**. Oikos, 106, 598–610. [http://doi.org/10.1111/j.0030-1299.2004.13043.x](http://doi.org/10.1111/j.0030-1299.2004.13043.x)\n\nEfford, M. G., \u0026 Dawson, D. K. (2009). **Effect of distance-related heterogeneity on population size estimates from point counts**. The Auk, 126(1), 100–111. http://doi.org/10.1525/auk.2009.07197\n\nEfford, M. G., Borchers, D. L., \u0026 Byron, A. E. (2009). **Density estimation by spatially explicit capture-recapture: Likelihood-based methods**. Environmental and Ecological Statistics. http://doi.org/10.1007/978-0-387-78151-8\n\nEfford, M. G., Dawson, D. K., \u0026 Borchers, D. L. (2009). **Population density estimated from locations of individuals on a passive detector array**. Ecology, 90(10), 2676–2682. http://doi.org/10.1890/08-1735.1\n\nEfford, M. G. (2011). **Estimation of population density by spatially explicit capture-recapture analysis of data from area searches**. Ecology, 92(12), 2202–2207. http://doi.org/10.1890/11-0332.1\n\nEfford, M. G., Borchers, D. L., \u0026 Mowat, G. (2013). **Varying effort in capture-recapture studies**. Methods in Ecology and Evolution, 4(7), 629–636. http://doi.org/10.1111/2041-210X.12049\n\nEfford, M. G., \u0026 Fewster, R. M. (2013). **Estimating population size by spatially explicit capture-recapture**. Oikos, 122(6), 918–928. http://doi.org/10.1111/j.1600-0706.2012.20440.x\n\nEfford, M., \u0026 Mowat, G. (2013). **Compensatory heterogeneity in spatially explicit capture− recapture data**. Ecology, 95(5), 1341–1348. http://doi.org/10.1890/13-1497.1\n\nEfford, M. G. (2014). **Bias from heterogeneous usage of space in spatially explicit capture-recapture analyses**. Methods in Ecology and Evolution, 5(7), 599–602. http://doi.org/10.1111/2041-210X.12169\n\nEfford, M. G., Dawson, D. K., Jhala, Y. V., \u0026 Qureshi, Q. (2015). **Density-dependent home-range size revealed by spatially explicit capture-recapture**. Ecography, n/a–n/a. http://doi.org/10.1111/ecog.01511\n\nFoster, R. J., \u0026 Harmsen, B. J. (2012). **A critique of density estimation from camera-trap data**. Journal of Wildlife Management, 76(2), 224–236. http://doi.org/10.1002/jwmg.275\n\nGalindo-Leal, C. (1990). **Live-trapping vs. snap-trapping of deer mice: a comparison of methods**. Acta Theriologica, 35(3-4), 357–363.\n\nGardner, B., Royle, J. A., \u0026 Wegan, M. T. (2009). **Hierarchical models for estimating density from DNA mark-recapture studies**. Ecology, 90(4), 1106–1115. http://doi.org/10.1890/07-2112.1\n\nGerber, B. D., Karpanty, S. M., \u0026 Kelly, M. J. (2012). **Evaluating the potential biases in carnivore capture-recapture studies associated with the use of lure and varying density estimation techniques using photographic-sampling data of the Malagasy civet**. Population Ecology, 54(1), 43–54. http://doi.org/10.1007/s10144-011-0276-3\n\nGerber, B. D., \u0026 Parmenter, R. R. (2015). **Spatial capture-recapture model performance with known small-mammal densities**. Ecological Applications, 25(3), 695–705. http://doi.org/10.1890/14-0960.1.sm\n\nGimenez, O., Choquet, R., Lamor, L., Scofield, P., Fletcher, D., Lebreton, J.-D., \u0026 Pradel, R. (2005). **Efficient profile-likelihood confidence intervals for capture-recapture models**. Journal of Agricultural, Biological, and Environmental Statistics, 10(2), 184–196. http://doi.org/10.1198/108571105X46462\n\nHanks, E. M., Hooten, M. B., Knick, S. T., Oyler-McCance, S. J., Fike, J. A., Cross, T. B., \u0026 Schwartz, M. K. (2016). **Latent spatial models and sampling design for landscape genetics**. The Annals of Applied Statistics, 10(2), 1041–1062. http://doi.org/10.1214/16-AOAS929\n\nHaynes, K. J., \u0026 Cronin, J. T. (2006). **Interpatch movement and edge effects: The role of behavioral responses to the landscape matrix.** Oikos, 113(1), 43–54. [http://doi.org/10.1111/j.0030-1299.2006.13977.x](http://doi.org/10.1111/j.0030-1299.2006.13977.x)\n\nIvan, J. S., White, G. C., \u0026 Shenk, T. M. (2013). **Using auxiliary telemetry information to estimate animal density from capture-recapture data**. Ecology, 94(4), 809–816. http://doi.org/10.1890/12-0101.1\n\nIvan, J. S., White, G. C., \u0026 Shenk, T. M. (2013). **Using simulation to compare methods for estimating density from capture-recapture data**. Ecology, 94(4), 817–826. http://doi.org/10.1890/12-0102.1\n\nKendall, W. L. (1999). **Robustness of closed capture-recapture methods to violations of the closure assumption**. Ecology, 80(8), 2517–2525. Retrieved from http://www.jstor.org/stable/177237\n\nKéry, M., Gardner, B., Stoeckle, T., Weber, D., \u0026 Royle, J. A. (2010). **Use of spatial capture-recapture modeling and DNA data to estimate densities of elusive animals**. Conservation Biology, 25(2), 356–364. http://doi.org/10.1111/j.1523-1739.2010.01616.x\n\nLinden, D. W., Sirén, A. P. K., \u0026 Pekins, P. J. (2018). **Integrating telemetry data into spatial capture-recapture modifies inferences on multi-scale resource selection**. Ecosphere, 9(4), e02203. http://doi.org/10.1002/ecs2.2203\n\nMarques, T. A., Thomas, L., \u0026 Royle, J. A. (2011). **A hierarchical model for spatial capture-recapture data: comment**. Ecology, 92(2), 526–528.\n\nManning, T., Edge, W. D., \u0026 Wolff, J. O. (1995). **Evaluating population-size estimators: an empirical approach**. Journal of Mammalogy, 76(4), 1149–1158.\n\nManning, J. a, \u0026 Goldberg, C. S. (2010). **Estimating population size using capture-recapture encounter histories created from point-coordinate locations of animals**. Methods in Ecology and Evolution, 1(4), 389–397. http://doi.org/10.1111/j.2041-210X.2010.00041.x\n\nMarucco, F., Boitani, L., Pletscher, D. H., \u0026 Schwartz, M. K. (2011). **Bridging the gaps between non-invasive genetic sampling and population parameter estimation**. European Journal of Wildlife Research, 57, 1–13. [http://doi.org/10.1007/s10344-010-0477-7](http://doi.org/10.1007/s10344-010-0477-7)\n\nMilleret, C., Dupont, P., Brøseth, H., Kindberg, J., Andrew Royle, J., \u0026 Bischof, R. (2018). *Using partial aggregation in Spatial Capture Recapture*. Methods in Ecology and Evolution. http://doi.org/10.1111/2041-210X.13030\n\nRamsey, D. S. L., Caley, P. A., \u0026 Robley, A. (2015). **Estimating population density from presence-absence data using a spatially explicit model**. Journal of Wildlife Management, 79(3), 491–499. http://doi.org/10.1002/jwmg.851\n\nReich, B. J., \u0026 Gardner, B. (2014). **A spatial capture-recapture model for territorial species**. Environmetrics, 1–9. Retrieved from http://arxiv.org/abs/1405.1976\n\nRowcliffe, J. M., Field, J., Turvey, S. T., \u0026 Carbone, C. (2008). **Estimating animal density using camera traps without the need for individual recognition**. Journal of Applied Ecology, 45(4), 1228–1236. http://doi.org/10.1111/j.1365-2664.2008.01473.x\n\nRoyle, J. A. (2004). **N-mixture models for estimating population size from spatially replicated counts**. Biometrics, 60(March), 108–115. Retrieved from https://classes.warnercnr.colostate.edu/bayes-workshop/files/2013/04/Royle_Biometrics_2004.pdf\n\nRoyle, J. A. (2004). **Generalized estimators of avian abundance from count survey data**. Animal Biodiversity and Conservation, 27(1), 375–386. Retrieved from http://abc.museucienciesjournals.cat/volum-27-1-2004-abc/generalized-estimators-of-avian-abundance-from-count-survey-data/?lang=en\n\nRoyle, J. A., \u0026 Young, K. V. (2008). **A hierarchical model for spatial capture recapture data**. Ecology, 89(8), 2281–2289. http://doi.org/10.1890/07-0601.1\n\nRoyle, A., Nichols, J. D., Karanth, K. U., \u0026 Gapalaswamy, A. M. (2009). **A hierarchical model for estimating density in camera-trap studies**. Journal of Applied Ecology, 46, 118–127. [http://doi.org/10.1111/j.1365-2664.2008.01578.x](http://doi.org/10.1111/j.1365-2664.2008.01578.x)\n\nRoyle, J. A., Karanth, K. U., Gopalaswamy, A. M., \u0026 Kumar, N. S. (2009). **Bayesian inference in camera trapping studies for a class of spatial capture-recapture models**. Ecology, 90(11), 3233–3244. http://doi.org/10.1890/08-1481.1\n\nRoyle, J. A. (2009). **Analysis of capture-recapture models with individual covariates using data augmentation**. Biometrics, 65(1), 267–274. http://doi.org/10.1111/j.1541-0420.2008.01038.x\n\nRoyle, J. A., Kéry, M., \u0026 Guélat, J. (2011). **Spatial capture-recapture models for search-encounter data**. 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(2017). **Evaluating camera traps as an alternative to live trapping for estimating the density of snowshoe hares (\u003ci\u003eLepus americanus\u003c/i\u003e) and red squirrels (\u003ci\u003eTamiasciurus hudsonicus\u003c/i\u003e)**. European Journal of Wildlife Research, 63(1), 7. http://doi.org/10.1007/s10344-016-1064-3\n\nWaits, L. P., \u0026 Paetkau, D. (2005). **Noninvasive Genetic Sampling Tools for Wildlife Biologists: a Review of Applications and Recommendations for Accurate Data Collection**. Journal of Wildlife Management, 69(4), 1419–1433. http://doi.org/10.2193/0022-541X(2005)69[1419:NGSTFW]2.0.CO;2\n\nWhittington, J., \u0026 Sawaya, M. A. (2015). **A comparison of grizzly bear demographic parameters estimated from non-spatial and spatial open population capture-recapture models**. PLoS ONE, 10(7), e0134446. http://doi.org/10.1371/journal.pone.0134446\n\nXiao, W., Feng, L., Mou, P. Miquelle, D. G., Hebblewhite, M., Goldberg, J. F., Robinson, H. S., Zhao, X., Zhou, B., Wang, T., Ge, J. (2016) **Estimating abundance and density of Amur tigers along the Sino-Russian border** [http://dx.doi.org/10.1111/1749-4877.12210](http://dx.doi.org/10.1111/1749-4877.12210)\n\n## Reports and other sources\nBlack Bear Population Size and Density in Apalachicola, Big Cypress, Eglin, Ocala/St. Johns, and Osceola Study Areas, Florida. [link](http://myfwc.com/media/4054764/finalpopulationestimatereport0816.pdf)\n\nWalker, Timothy A. (2016) Testing camera trap density estimates from the spatial capture model and calibrated capture rate indices against kangaroo rat (\u003ci\u003eDipodomys\u003c/i\u003e spp.) live trapping data. Master of science thesis [link](http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=8289\u0026context=etd_theses)\n\n[web] [WILD8390 R code to simulate common data structures in R and perform MLE from simulated data](https://sites.google.com/site/wild8390/software/simulate)\n\nSmith, Jennifer B. 2018. Context Matters for Black Bears: Evaluating Spatially Explicit Density Estimators and Trade-Offs in Resource Selection. Michigan State University, ProQuest Dissertations Publishing. 10747191\n[link](https://search.proquest.com/openview/09f193505767ffcffcdf8cf37038699b/1?pq-origsite=gscholar\u0026cbl=18750\u0026diss=y)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fromunov%2Fsecr_resources","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fromunov%2Fsecr_resources","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fromunov%2Fsecr_resources/lists"}