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https://github.com/romunov/secr_resources

Resources that might come handy to anyone using spatially explicit mark-capture-recapture models.
https://github.com/romunov/secr_resources

capture-recapture-models density-estimation ecology hierarchical-models population-density population-size spatially-explicit-models

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Resources that might come handy to anyone using spatially explicit mark-capture-recapture models.

Host: GitHub
URL: https://github.com/romunov/secr_resources
Owner: romunov
Created: 2016-05-07T12:01:04.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2019-06-15T18:17:49.000Z (over 5 years ago)
Last Synced: 2024-01-30T05:10:05.207Z (9 months ago)
Topics: capture-recapture-models, density-estimation, ecology, hierarchical-models, population-density, population-size, spatially-explicit-models
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Metadata Files:
- Readme: README.md

Awesome Lists containing this project

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.

# Books
Royle, 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))

Williams, B., Nichols, J., & 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

# (R) resources
Augustine, B. and Royle, A. (2016) **SPIM: Open population SCR MCMC sampler**. [R package available on GitHub](https://github.com/benaug/SPIM)

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

Morin, D., Fuller, A. K., Royle, J. A., & 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

Moya, Ó., Mansilla, P.-L., Madrazo, S., Igual, J.-M., Rotger, A., Romano, A., & 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

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

Swinnen, K. R. R., Reijniers, J., Breno, M., & 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

# Papers
## Methodological

Augustine, B. C., Royle, J. A., Kelly, M. J., Satter, C. B., Alonso, R. S., & 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))

Moqanaki, E. M., Jiménez, J., & López-Bao, J. V. (2018). **Counting bears in the Iranian Caucasus : Remarkable mismatch between scientifically-sound population estimates and perceptions**. Biological Cons

Benhamou, 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)

Boulanger, J., & 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)

Borchers, D. L., & 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

Borchers, D. (2012). **A non-technical overview of spatially explicit capture-recapture models**. Journal of Ornithology. http://doi.org/10.1007/s10336-010-0583-z

Borchers, D. L., & Fewster, R. M. (2013). **Spatial capture-recapture models**. Statistical Science, 1–20. http://doi.org/10.1016/B978-0-12-405939-9.00020-7

Borchers, D., Distiller, G., Foster, R., Harmsen, B., & 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

Borchers, D. L., Stevenson, B. C., Kidney, D., Thomas, L., & 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

Borchers, D. L., & 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

Bozarth, C. A., Gardner, B., Rockwood, L. L., & 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

Chandler, R. B., Royle, J. A., & 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

Chandler, R. B., & 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

Chandler, R. B., & 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

Chandler, R. B., Hepinstall-Cymerman, J., Merker, S., Abernathy-Conners, H., & 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

Crimmins, S. M., Walleser, L. R., Hertel, D. R., McKann, P. C., Rohweder, J. J., & 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

Davidson, G. A., Clark, D. A., Johnson, B. K., Waits, L. P., & 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

Dey, S., Delampady, M., Karanth, K. U., & 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

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

Drewry, J. M., Van Manen, F. T., & 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

Dorazio, 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

Dorazio, 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

Dorazio, 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

Dutta, T., Sharma, S., Maldonado, J. E., Wood, T. C., Panwar, H. S., & 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

Efford, 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)

Efford, M. G., & 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

Efford, M. G., Borchers, D. L., & 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

Efford, M. G., Dawson, D. K., & 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

Efford, 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

Efford, M. G., Borchers, D. L., & 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

Efford, M. G., & 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

Efford, M., & Mowat, G. (2013). **Compensatory heterogeneity in spatially explicit capture− recapture data**. Ecology, 95(5), 1341–1348. http://doi.org/10.1890/13-1497.1

Efford, 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

Efford, M. G., Dawson, D. K., Jhala, Y. V., & 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

Foster, R. J., & 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

Galindo-Leal, C. (1990). **Live-trapping vs. snap-trapping of deer mice: a comparison of methods**. Acta Theriologica, 35(3-4), 357–363.

Gardner, B., Royle, J. A., & 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

Gerber, B. D., Karpanty, S. M., & 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

Gerber, B. D., & 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

Gimenez, O., Choquet, R., Lamor, L., Scofield, P., Fletcher, D., Lebreton, J.-D., & 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

Hanks, E. M., Hooten, M. B., Knick, S. T., Oyler-McCance, S. J., Fike, J. A., Cross, T. B., & 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

Haynes, K. J., & 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)

Ivan, J. S., White, G. C., & 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

Ivan, J. S., White, G. C., & 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

Kendall, 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

Kéry, M., Gardner, B., Stoeckle, T., Weber, D., & 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

Linden, D. W., Sirén, A. P. K., & 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

Marques, T. A., Thomas, L., & Royle, J. A. (2011). **A hierarchical model for spatial capture-recapture data: comment**. Ecology, 92(2), 526–528.

Manning, T., Edge, W. D., & Wolff, J. O. (1995). **Evaluating population-size estimators: an empirical approach**. Journal of Mammalogy, 76(4), 1149–1158.

Manning, J. a, & 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

Marucco, F., Boitani, L., Pletscher, D. H., & 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)

Milleret, C., Dupont, P., Brøseth, H., Kindberg, J., Andrew Royle, J., & Bischof, R. (2018). *Using partial aggregation in Spatial Capture Recapture*. Methods in Ecology and Evolution. http://doi.org/10.1111/2041-210X.13030

Ramsey, D. S. L., Caley, P. A., & 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

Reich, B. J., & Gardner, B. (2014). **A spatial capture-recapture model for territorial species**. Environmetrics, 1–9. Retrieved from http://arxiv.org/abs/1405.1976

Rowcliffe, J. M., Field, J., Turvey, S. T., & 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

Royle, 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

Royle, 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

Royle, J. A., & 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

Royle, A., Nichols, J. D., Karanth, K. U., & 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)

Royle, J. A., Karanth, K. U., Gopalaswamy, A. M., & 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

Royle, 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

Royle, J. A., Kéry, M., & Guélat, J. (2011). **Spatial capture-recapture models for search-encounter data**. Methods in Ecology and Evolution, 2(6), 602–611. http://doi.org/10.1111/j.2041-210X.2011.00116.x

Royle, J. A., & Dorazio, R. M. (2012). **Parameter-expanded data augmentation for Bayesian analysis of capture-recapture models**. Journal of Ornithology, 152(SUPPL. 2), 521–537. http://doi.org/10.1007/s10336-010-0619-4

Royle, J. A., Chandler, R. B., Yackulic, C., & Nichols, J. D. (2012). **Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions**. Methods in Ecology and Evolution, 3(3), 545–554. http://doi.org/10.1111/j.2041-210X.2011.00182.x

Royle, J. A., Chandler, R. B., Gazenski, K. D., & Graves, T. A. (2013). **Spatial capture-recapture models for jointly estimating population density and landscape connectivity**. Ecology, 94(2), 287–294. http://doi.org/10.1890/12-0413.1

Royle, J. A., Chandler, R. B., Sun, C. C., & Fuller, A. K. (2013). **Integrating resource selection information with spatial capture-recapture**. Methods in Ecology and Evolution, 4(6), 520–530. http://doi.org/10.1111/2041-210X.12039

Royle, J. A., & Converse, S. J. (2014). **Hierarchical spatial capture-recapture models: Modelling population density in stratified populations**. Methods in Ecology and Evolution, 5(1), 37–43. http://doi.org/10.1111/2041-210X.12135

Royle, J. A., Chandler, R. B., Sun, C. C., & Fuller, A. K. (2014). **Reply to Efford on “Integrating resource selection information with spatial capture-recapture”**. Methods in Ecology and Evolution, 5(7), 603–605. http://doi.org/10.1111/2041-210X.12205

Royle, J. A., Fuller, A. K., & Sutherland, C. (2016). **Spatial capture–recapture models allowing Markovian transience or dispersal**. Population Ecology, 58(1), 53–62. http://doi.org/10.1007/s10144-015-0524-z

Royle, J. A., Fuller, A. K., & Sutherland, C. (2017). **Unifying Population and Landscape Ecology with Spatial Capture-recapture**. bioRxiv, 31. http://doi.org/10.1101/103341

Sollmann, R., Tôrres, N. M., Furtado, M. M., De Almeida Jácomo, A. T., Palomares, F., Roques, S., & Silveira, L. (2013). **Combining camera-trapping and noninvasive genetic data in a spatial capture-recapture framework improves density estimates for the jaguar**. Biological Conservation, 167, 242–247. http://doi.org/10.1016/j.biocon.2013.08.003

Sollmann, R., Gardner, B., & Belant, J. L. (2012). **How does spatial study design influence density estimates from spatial capture-recapture models**? PLoS ONE, 7(4), 1–8. http://doi.org/10.1371/journal.pone.0034575

Speed, C. W., Meekan, M. G., & Bradshaw, C. J. A. (2007). **Spot the match - wildlife photo-identification using information theory**. Frontiers in Zoology, 4, 2. http://doi.org/10.1186/1742-9994-4-2

Spehar, S. N., Loken, B., Rayadin, Y., & Royle, J. A. (2015). **Comparing spatial capture-recapture modeling and nest count methods to estimate orangutan densities in the Wehea Forest, East Kalimantan, Indonesia**. Biological Conservation, 191(February 2016), 185–193. http://doi.org/10.1016/j.biocon.2015.06.013

Sun, C. C., Fuller, A. K., & Andrew Royle, J. (2014). **Trap configuration and spacing influences parameter estimates in spatial capture-recapture models**. PLoS ONE, 9(2), 1–9. http://doi.org/10.1371/journal.pone.0088025

Thompson, C. M., Royle, J. A., & Garner, J. D. (2012). **A framework for inference about carnivore density from unstructured spatial sampling of scat using detector dogs**. Journal of Wildlife Management, 76(4), 863–871. http://doi.org/10.1002/jwmg.317

Tallmon, D. A., & Mills, L. S. (2004). **Edge effects and isolation: red-backed voles revisited**. Conservation Biology, 18(6), 1658–1664. [http://doi.org/10.1111/j.1523-1739.2004.00439.x](http://doi.org/10.1111/j.1523-1739.2004.00439.x)

Wilton, C. M., Puckett, E. E., Beringer, J., Gardner, B., Eggert, L. S., & Belant, J. L. (2014). **Trap Array Configuration Influences Estimates and Precision of Black Bear Density and Abundance**. PLoS ONE, 9(10), e111257. http://doi.org/10.1371/journal.pone.0111257

Wilton, C. M., Beringer, J., Puckett, E. E., Eggert, L. S., & Belant, J. L. (2016). **Spatiotemporal factors affecting detection of black bears during noninvasive capture-recapture surveys**. Journal of Mammalogy, 97(1), 266–273. http://doi.org/10.1093/jmammal/gyv176

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Tenan, S., Pedrini, P., Bragalanti, N., Groff, C., & Sutherland, C. (2017). **Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency**. PLOS ONE, 12(10), e0185588. https://doi.org/10.1371/journal.pone.0185588

Xu, C., Sun, D., & He, C. (2014). **Objective Bayesian analysis for a capture-recapture model**. Annals of the Institute of Statistical Mathematics, 66(2), 245–278. http://doi.org/10.1007/s10463-013-0413-1

Xue, Y., Fuller, A., Royle, J. A., & Gomes, C. P. (2017). **Dynamic Optimization of Landscape Connectivity Embedding Spatial-Capture-Recapture Information Auto Converge to the Minimal Resistance Path**. Retrieved from http://www.cs.cornell.edu/~yexiang/publications/aaai17_scr_connectivity_xor.pdf

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Zhao, Q., Royle, J. A., & Boomer, G. S. (2017). **Spatially explicit dynamic N-mixture models**. Population Ecology, 1–8. http://doi.org/10.1007/s10144-017-0600-7

Zipkin, E. F., Sillett, T. S., Grant, E. H. C., Chandler, R. B., & Royle, J. A. (2013). **Inferences about population dynamics from count data using multistate models: a comparison to capture-recpature approaches**. Ecology and Evolution, 1–10. [http://doi.org/10.1002/ece3.942](http://doi.org/10.1002/ece3.942)

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## Application

Anile, S., Ragni, B., Randi, E., Mattucci, F., & Rovero, F. (2014). **Wildcat population density on the Etna volcano, Italy: A comparison of density estimation methods**. Journal of Zoology, 293(4), 252–261. http://doi.org/10.1111/jzo.12141

Arechavala-Lopez, P., Minguito-Frutos, M., Follana-Berná, G., & Palmer, M. (2018). **Common octopus settled in human-altered Mediterranean coastal waters: from individual home-range to population dynamic**. ICES Journal of Marine Science. http://doi.org/10.1093/icesjms/fsy014

Avgan, B., Zimmermann, F., Güntert, M., Arıkan, F., & Breitenmoser, U. (2014). **The first density estimation of an isolated Eurasian lynx population in southwest Asia**. Wildlife Biology, 20(4), 217–221. http://doi.org/10.2981/wlb.00025

Beausoleil, R. A., Clark, J. D., & Maletzke, B. T. (2016). **A long-term evaluation of biopsy darts and DNA to estimate cougar density: An agency-citizen science collaboration**. Wildlife Society Bulletin. http://doi.org/10.1002/wsb.675

Beaver, J. T., Harper, C. A., Muller, L., Basinger, P. S., Goode, M. J., & Van Manen, F. T. (2016). **Current and Spatially Explicit Capture-recapture Analysis Methods for Infrared Triggered Camera Density Estimation of White-tailed Deer**. Journal of the Southeastern Association of Fish and Wildlife Agencies, 3(March), 195–202.

Berl, J. L., Kellner, K. F., Flaherty, E. A., & Swihart, R. K. (2018). **Spatial Variation in Density of White-footed Mice Along Edges in Fragmented Habitat**. The American Midland Naturalist, 179(1), 38–50. http://doi.org/10.1674/0003-0031-179.1.38

Blanc, L., Marboutin, E., Gatti, S., & Gimenez, O. (2013). **Abundance of rare and elusive species: Empirical investigation of closed versus spatially explicit capture-recapture models with lynx as a case study**. Journal of Wildlife Management, 77(2), 372–378. http://doi.org/10.1002/jwmg.453

Broekhuis, F., & Gopalaswamy, A. M. (2016). **Counting cats: spatially explicit population estimates of cheetah (Acinonyx jubatus) using unstructured sampling data**. PLoS ONE, 11(5), e0153875. http://doi.org/10.1371/journal.pone.0153875

Chabanne, D. B. H., Pollock, K. H., Finn, H., & Bejder, L. (2017). **Applying the Multistate Capture-recapture Robust Design to characterize metapopulation structure**. Methods in Ecology and Evolution. http://doi.org/10.1111/2041-210X.12792

Christiansen, F., Bertulli, C. G., Rasmussen, M. H., & Lusseau, D. (2015). **Estimating cumulative exposure of wildlife to non-lethal disturbance using spatially explicit capture-recapture models**. Journal of Wildlife Management. http://doi.org/10.1002/jwmg.836

Clare, J. D. J., Anderson, E. M., & MacFarland, D. M. (2015). **Predicting bobcat abundance at a landscape scale and evaluating occupancy as a density index in central Wisconsin**. Journal of Wildlife Management, 79(3), 469–480. http://doi.org/10.1002/jwmg.844

Devens, C., Tshabalala, T., McManus, J., & Smuts, B. (2018). **Counting the spots: The use of a spatially explicit capture-recapture technique and GPS data to estimate leopard (_Panthera pardus_) density in the Eastern and Western Cape, South Africa**. African Journal of Ecology. http://doi.org/10.1111/aje.12512

Dou, H., Yang, H., Feng, L., Mou, P., Wang, T., & Ge, J. (2016). **Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China**. PloS One, 11(4), e0154254. http://doi.org/10.1371/journal.pone.0154254

Evans, M. J., Rittenhouse, T. A. G., Hawley, J. E., & Rego, P. W. (2017). **Black bear recolonization patterns in a human-dominated landscape vary based on housing: New insights from spatially explicit density models**. Landscape and Urban Planning, 162, 13–24. http://doi.org/10.1016/J.LANDURBPLAN.2017.01.009

Fuller, A. K., Sutherland, C. S., Royle, J. A., & Hare, M. P. (2015). **Estimating population density and connectivity of American mink using spatial capture-recapture**. Ecological Applications, 26(4), 15–0315.1. http://doi.org/10.1890/15-0315.1

Goode, M. J., Beaver, J. T., Muller, L. I., Clark, J. D., Manen, F. T. van, Harper, C. A., & Basinger, P. S. (2014). **Capture—recapture of white-tailed deer using DNA from fecal pellet groups**. Wildlife Biology, 20(5), 270–278. http://doi.org/10.2981/wlb.00050

Granjon, A.-C., Rowney, C., Vigilant, L., & Langergraber, K. E. (2016). **Evaluating genetic capture-recapture using a chimpanzee population of known size**. The Journal of Wildlife Management. http://doi.org/10.1002/jwmg.21190

Gopalaswamy, A. M., Royle, J. A., Delampady, M., Nichols, J. D., Karanth, K. U., & Macdonald, D. W. (2012). **Density estimation in tiger populations: combining information for strong inference**. Ecology, 93(7), 1741–1751. http://doi.org/10.1890/11-2110.1

Jiménez, J., Higuero, R., Charre-Medellin, J. F., & Acevedo, P. (2017). **Spatial mark-resight models to estimate feral pig population density**. Hystrix, (September), 1–6. http://doi.org/10.4404/hystrix-28.2-12141

Jůnek, T., Jůnková Vymyslická, P., Hozdecká, K., & Hejcmanová, P. (2015). **Application of Spatial and Closed Capture-Recapture Models on Known Population of the Western Derby Eland (Taurotragus derbianus derbianus) in Senegal**. PLOS ONE, 10(9), e0136525. http://doi.org/10.1371/journal.pone.0136525

Karanth, K. U., Chundawat, R. S., Nichols, J. D., & Kumar, N. S. (2004). **Estimation of tiger densities in the tropical dry forests of Panna, Central India, using photographic capture–recapture sampling**. Animal Conservation, 7(3), 285–290. http://doi.org/10.1017/S1367943004001477

Kristensen, T. V., & Kovach, A. I. (2018). **Spatially explicit abundance estimation of a rare habitat specialist: implications for SECR study design**. Ecosphere, 9(May), e02217.10.1002. http://doi.org/10.1002/ecs2.2217

Linden, D. W., Fuller, A. K., Royle, J. A., & Hare, M. P. (2017). **Examining the occupancy–density relationship for a low-density carnivore**. Journal of Applied Ecology, 54(6), 2043–2052. http://doi.org/10.1111/1365-2664.12883

Linkie, M., Guillera-Arroita, G., Smith, J., & Rayan, D. M. (2010). **Monitoring tigers with confidence**. Integrative Zoology, 5(4), 342–350. http://doi.org/10.1111/j.1749-4877.2010.00215.x

Manning, J. A., & 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](http://doi.org/10.1111/j.2041-210X.2010.00041.x)

Majumder, A., Qureshi, Q., Sankar, K., & Kumar, A. (2017). **Long-term monitoring of a Bengal tiger (Panthera tigris tigris) population in a human-dominated landscape of Central India**. European Journal of Wildlife Research, 63(1), 17. http://doi.org/10.1007/s10344-016-1070-5

Morin, D. J., Waits, L. P., McNitt, D. C., & Kelly, M. J. (2018). Efficient single-survey estimation of carnivore density using fecal DNA and spatial capture-recapture: a bobcat case study. Population Ecology, 1–13. http://doi.org/10.1007/s10144-018-0606-9

Muneza, A. B., Linden, D. W., Montgomery, R. A., Dickman, A. J., Roloff, G. J., Macdonald, D. W., & Fennessy, J. T. (2016). **Examining disease prevalence for species of conservation concern using non-invasive spatial capture-recapture techniques**. Journal of Applied Ecology. http://doi.org/10.1111/1365-2664.12796

Mollet, P., Kéry, M., Gardner, B., Pasinelli, G., & Royle, J. A. (2015). **Estimating population size for capercaillie (Tetrao urogallus L.) with spatial capture-recapture models based on genotypes from one field sample**. PLoS ONE, 10(6), 1–16. http://doi.org/10.1371/journal.pone.0129020

Morehouse, A. T., & Boyce, M. S. (2016). **Grizzly bears without borders: Spatially explicit capture-recapture in southwestern Alberta**. The Journal of Wildlife Management. http://doi.org/10.1002/jwmg.21104

Murphy, S. M., Cox, J. J., Augustine, B. C., Hast, J. T., Guthrie, J. M., Wright, J., … Plaxico, J. H. (2016). **Characterizing recolonization by a reintroduced bear population using genetic spatial capture-recapture.** The Journal of Wildlife Management, 1–18. http://doi.org/10.1002/jwmg.21144

O’Mahony, D. T., Powell, C., Power, J., Hanniffy, R., Marnell, F., Turner, P., & O’Reilly, C. (2017). **Non-invasively determined multi-site variation in pine marten Martes martes density, a recovering carnivore in Europe**. European Journal of Wildlife Research, 63(3), 48. http://doi.org/10.1007/s10344-017-1108-3

Pirotta, E., Thompson, P. M., Cheney, B., Donovan, C. R., & Lusseau, D. (2015). **Estimating spatial, temporal and individual variability in dolphin cumulative exposure to boat traffic using spatially explicit capture-recapture methods**. Animal Conservation, 18(1), 20–31. http://doi.org/10.1111/acv.12132

Pesenti, E., & Zimmermann, F. (2013). **Density estimations of the Eurasian lynx (Lynx lynx) in the Swiss Alps**. Journal of Mammalogy, 94(1), 73–81. http://doi.org/10.1644/11-MAMM-A-322.1

Potts, J. M., Buckland, S. T., Thomas, L., & Savage, A. (2016). **Estimating Key Largo woodrat abundance using spatially explicit capture-recapture and trapping point transects**. Wildlife Society Bulletin. http://doi.org/10.1002/wsb.651

Rich, L. N., Kelly, M. J., Sollmann, R., Noss, A. J., Maffei, L., Arispe, R. L., … Di Bitetti, M. S. (2014). **Comparing capture–recapture, mark–resight, and spatial mark–resight models for estimating puma densities via camera traps**. Journal of Mammalogy, 95(2), 382–391. http://doi.org/10.1644/13-MAMM-A-126

Rodgers, T. W., Giacalone, J., Heske, E. J., Janečka, J. E., Phillips, C. a, Schooley, R. L., & Rodgers, W. (2014). **Comparison of noninvasive genetics and camera trapping for estimating population density of ocelots (_Leopardus pardalis_) on Barro Colorado Island, Panama**. Tropical Conservation Science, 777(444), 690–705. Retrieved from www.tropicalconservationscience.org

Roffler, G. H., Waite, J. N., Flynn, R. W., & Larson, K. R. (2016). **Estimation of wolf population density using spatial capture-recapture: refining methods for monitoring cryptic species**. In Columbia Mountain Institute of Applied Ecology Predator-Prey Dynamics: From Theory to Management conference. PeerJ Inc. http://doi.org/10.1017/CBO9781107415324.004

Schmidt, B. R., Meier, A., Sutherland, C., & Royle, J. A. (2017). **Spatial capture – recapture analysis of artificial cover board survey data reveals small scale spatial variation in slow-worm Anguis fragilis density**. Royal Society Open Science, 4(9), 170374. https://doi.org/10.1098/rsos.170374

Seymour, A. S., Tarrant, M. R., Gerber, B. D., Sharp, A., Woollam, J., & Cox, R. (2017). **Effects of El Niño on the population dynamics of the Malay civet east of the Wallace line**. Journal of Zoology. http://doi.org/10.1111/jzo.12469

Sollmann, R., Gardner, B., Belant, J. L., Wilton, C. M., & Beringer, J. (2016). **Habitat associations in a recolonizing , low- density black bear population.** Ecosphere, 7(August), 1–11. http://doi.org/10.1002/ecs2.1406

Stetz, J. B., Mitchell, M. S., & Kendall, K. C. (2018). **Using Spatially-Explicit Capture-Recapture Models to Explain Variation in Seasonal Density Patterns of Sympatric Ursids**. Ecography. http://doi.org/10.1111/ecog.03556

Rehnus, M., & Bollmann, K. (2016). **Non-invasive genetic population density estimation of mountain hares (Lepus timidus) in the Alps: systematic or opportunistic sampling?** European Journal of Wildlife Research. http://doi.org/10.1007/s10344-016-1053-6

Royle, J. A., Magoun, A. J., Gardner, B., Valkenburg, P., & Lowell, R. E. (2011). **Density estimation in a wolverine population using spatial capture-recapture models**. Journal of Wildlife Management, 75(3), 604–611. http://doi.org/10.1002/jwmg.79

Russell, R. E., Royle, J. A., Desimone, R., Schwartz, M. K., Edwards, V. L., Pilgrim, K. P., & McKelvey, K. S. (2012). **Estimating abundance of mountain lions from unstructured spatial sampling**. Journal of Wildlife Management, 76(8), 1551–1561. http://doi.org/10.1002/jwmg.412

Sarmento, P., Cruz, J., Eira, C., & Fonseca, C. (2014). **A spatially explicit approach for estimating space use and density of common genets Portugal**. Animal Biodiversity and Conservation, 37(1), 23–33. Retrieved from http://www.raco.cat/index.php/ABC/article/view/278388

Selvan, K. M., Lyngdoh, S., Habib, B., & Gopi, G. V. (2014). **Population density and abundance of sympatric large carnivores in the lowland tropical evergreen forest of Indian Eastern Himalayas**. Mammalian Biology - Zeitschrift Für Säugetierkunde, 79(4), 254–258. http://doi.org/10.1016/j.mambio.2014.03.002

Sharma, R. K., Jhala, Y., Qureshi, Q., Vattakaven, J., Gopal, R., & Nayak, K. (2010). **Evaluating capture-recapture population and density estimation of tigers in a population with known parameters**. Animal Conservation, 13(1), 94–103. http://doi.org/10.1111/j.1469-1795.2009.00305.x

Sugimoto, T., Nagata, J., Aramilev, V. V., & McCullough, D. R. (2012). **Population size estimation of Amur tigers in Russian Far East using noninvasive genetic samples**. Journal of Mammalogy, 93(1), 93–101. http://doi.org/10.1644/10-MAMM-A-368.1

Tobler, M. W., & Powell, G. V. N. (2013). **Estimating jaguar densities with camera traps: Problems with current designs and recommendations for future studies**. Biological Conservation, 159, 109–118. http://doi.org/10.1016/j.biocon.2012.12.009

Trolle, M., & Kéry, M. (2003). **Estimation of ocelot density in the Pantanal using capture-recapture analysis of camera-trapping data**. Journal of Mammalogy, 84(2), 607–614. http://doi.org/10.1644/1545-1542(2003)084<0607:EOODIT>2.0.CO;2

Villela, D. A. M., Codeço, C. T., Figueiredo, F., Garcia, G. A., Maciel-de-Freitas, R., & Struchiner, C. J. (2015). **A Bayesian hierarchical model for estimation of abundance and spatial density of *Aedes aegypti***. PLoS ONE, 10(4), e0123794. http://doi.org/10.1371/journal.pone.0123794

Villette, P., Krebs, C. J., & Jung, T. S. (2017). **Evaluating camera traps as an alternative to live trapping for estimating the density of snowshoe hares (Lepus americanus) and red squirrels (Tamiasciurus hudsonicus)**. European Journal of Wildlife Research, 63(1), 7. http://doi.org/10.1007/s10344-016-1064-3

Waits, L. P., & 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

Xiao, 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)

## Reports and other sources
Black 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)

Walker, Timothy A. (2016) Testing camera trap density estimates from the spatial capture model and calibrated capture rate indices against kangaroo rat (Dipodomys spp.) live trapping data. Master of science thesis [link](http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=8289&context=etd_theses)

[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)

Smith, 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
[link](https://search.proquest.com/openview/09f193505767ffcffcdf8cf37038699b/1?pq-origsite=gscholar&cbl=18750&diss=y)