Patuxent Wildlife Research Center

whiteshadow
Patuxent Intranet | Patuxent Home | Staff | Contact Us  
Back

J. Andy Royle

Email: aroyle@usgs.gov

Areas of Study

Hierarchical Models of Animal Abundance and Occurrence

Estimating Trend and Detection Probability Using Data from the Breeding Bird Survey

Estimation of Population Densities for the Florida Panther

Spatial Capture-Recapture Models to Estimate Abundance and Density of Animal Populations

Books

Royle, J. A., R. B. Chandler, R. Sollmann, and B. Gardner. 2014. Spatial Capture-Recapture. . Academic Press, Waltham, MA. xxix, 577 pp. Abstract

Publications

2014

Cohen, E. B., J. A. Hostetler, J. A. Royle, and P. P. Marra. 2014. Estimating migratory connectivity of birds when re-encounter probabilities are heterogeneous. Ecology and Evolution 4(9):1659-1670. Abstract

Fiske, I. J., J. A. Royle, and K. Gross. 2014. Inference for finite-sample trajectories in dynamic multi-state site-occupancy models using hidden Markov model smoothing. Environmental and Ecological Statistics 21(2):313-328. Abstract

Royle, J. A., R. B. Chandler, R. Sollmann, and B. Gardner. 2014. Spatial Capture-Recapture. Academic Press, Waltham, MA. xxix, 577 pp. Abstract

Royle, J. A., R. B. Chandler, C. C. Sun, and A. K. Fuller. 2014. Reply to Efford on “Integrating Resource Selection Information with Spatial Capture-Recapture". Methods in Ecology and Evolution Online Early Abstract

Royle, J. A. and S. J. Converse. 2014. Hierarchical spatial capture–recapture models: modelling population density in stratified populations. Methods in Ecology and Evolution 5(1):37-43. Abstract

Sun, C. C., A. K. Fuller, and J. A. Royle. 2014. Trap Configuration and Spacing Influences Parameter Estimates in Spatial Capture-Recapture Models. PLoS ONE 9(2):e88025. Abstract

Zipkin, E. F., T. S. Sillett, E. H. C. Grant, R. B. Chandler, and J. A. Royle. 2014. Inferences about population dynamics from count data using multistate models: a comparison to capture–recapture approaches. Ecology and Evolution 4(4):417-426. Abstract

Zipkin, E. F., J. T. Thorson, K. See, H. J. Lynch, E. H. C. Grant, Y. Kanno, R. B. Chandler, B. H. Letcher, and J. A. Royle. 2014. Modeling structured population dynamics using data from unmarked individuals. Ecology 95(1):22-29. Abstract

2013

Bled, F., J. R. Sauer, K. L. Pardieck, P. Doherty, and J. A. Royle. 2013. Modeling Trends from North American Breeding Bird Survey Data: A Spatially Explicit Approach. PLOS ONE 8(12):e81867. Abstract

Boomer, G. S., G. S. Zimmerman, N. L. Zimpfer, P. R. Garrettson, M. D. Koneff, T. A. Sanders, K. D. Magruder, and J. A. Royle. 2013. Band reporting probabilities for mallards recovered in the United States and Canada. Journal of Wildlife Management 77(5):1059-1066. Abstract

Cam, E., O. Gimenez, R. Alpizar-Jara, L. M. Aubry, M. Authier, E. G. Cooch, D. N. Koons, W. A. Link, J.-Y. Monnat, J. D. Nichols, J. J. Rotella, J. A. Royle, and R. Pradel. 2013. Looking for a needle in a haystack: Inference about individual fitness components in a heterogeneous population. Oikos 122(5):739-753. Abstract

Chandler, R. B. and J. A. Royle. 2013. Spatially explicit models for inference about density in unmarked or partially marked populations. Annals of Applied Statistics 7(2):936-954. Abstract

Converse, S. J., J. A. Royle, P. H. Adler, R. P. Urbanek, and J. A. Barzen. 2013. A hierarchical nest survival model integrating incomplete temporally varying covariates. Ecology and Evolution 3 (13):4439-4447. Abstract

Fukaya, K. and J. A. Royle. 2013. Markov models for community dynamics allowing for observation error. Ecology 94(12):2670-2677. Abstract

Graves, T. A., P. Beier, and J. A. Royle. 2013. Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal . Molecular Ecology 22(15):3888-3903. Abstract

Mattsson, B. J., E. F. Zipkin, B. Gardner, P. J. Blank, J. R. Sauer, and J. A. Royle. 2013. Explaining local-scale species distributions: Relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage. PLoS ONE 8(2):e55097. Abstract

Royle, J. A., R. B. Chandler, K. Gazenski, and T. A. Graves. 2013. Spatial capture-recapture models for jointly estimating population density and landscape connectivity. Ecology 94(2):287-294. Abstract

Royle, J. A., R. B. Chandler, C. C. Sun, and A. K. Fuller. 2013. Integrating resource selection information with spatial capture-recapture. Methods in Ecology and Evolution 4(6):520-530. Abstract

Schaub, M. and J. A. Royle. 2013. Estimating true instead of apparent survival using spatial Cormack-Jolly-Seber models. Methods in Ecology and Evolution Online Early November 29 Abstract

Sollmann, R., B. Gardner, R. B. Chandler, D. B. Shindle, D. P. Onorato, J. A. Royle, and A. F. O'Connell. 2013. Using multiple data sources provides density estimates for endangered Florida panther. Journal of Applied Ecology. 50(4):961-968. Abstract

Tenan, S., A. Rotger Vallespir, J. M. Igual, T. Moya, J. A. Royle, and G. Tavecchia. 2013. Population abundance, size structure and sex-ratio in an insular lizard. Ecological Modelling 267:39-47. Abstract

Yackulic, C., R. Chandler, E. F. Zipkin, J. A. Royle, J. D. Nichols, E. H. C. Grant, and S. Veran. 2013. Presence-only modeling using MAXENT: when can we trust the inferences? Methods in Ecology and Evolution 4(3):236-243. Abstract

2012

Converse, S. J. and J. A. Royle. 2012. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations. Pages 427-442 in Robert A. Gitzen, Joshua J. Millspaugh, Andrew B. Cooper, and Daniel S. Licht, editors. Design and analysis of long-term ecological monitoring studies. Cambridge University Press, New York. xxiv, 560 pp. Abstract

Converse, S. J., J. A. Royle, and R. P. Urbanek. 2012. Bayesian analysis of multi-state data with individual covariates for estimating genetic effects on demography. Pages S561-S572 in Michael Schaub and William L. Kendall, editors. Proceedings EURING Analytical Conference 2009: Estimation, modelling and conservation of vertebrate populations using marked individuals. Journal of Ornithology 152(Supplement 2) Abstract

Gopalaswamy, A. M., J. A. Royle, M. Delampady, J. D. Nichols, K. U. Karanth, and D. W. MacDonald. 2012. Density estimation in tiger populations: combining information for strong inference. Ecology 93(7):1741-1751. Abstract

Gopalaswamy, A. M., J. A. Royle, J. E. Hines, P. Singh, D. Jathanna, N. S. Kumar, and K. U. Karanth. 2012. Program SPACECAP: Software for estimating animal density using spatially explicit capture-recapture models. Methods in Ecology and Evolution 3(6):1067-1072. Abstract

Graves, T. A., J. A. Royle, K. C. Kendall, P. Beier, J. B. Stetz, and A. Macleod. 2012. Balancing precision and risk: Should multiple detection methods be analyzed separately in N-mixture models? PLoS ONE 7(12):1-9, e49410. Abstract

Lyons, J. E., J. A. Royle, S. M. Thomas, E. Elliott-Smith, Evenson J.R., E. G. Kelly, R. L. Milner, D. R. Nysewander, and B. A. Andres. 2012. Large-scale monitoring of shorebird populations using count data and N-mixture models: Black Oystercatcher (Haematopus bachmani) surveys by land and sea. Auk 129(4):645-652. Abstract

Padding, P. I. and J. A. Royle. 2012. Assessment of bias in US waterfowl harvest estimates. Wildlife Research 39(4):336-342. Abstract

Royle, J. A., R. B. Chandler, C. Yackulic, and J. D. Nichols. 2012. Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods in Ecology and Evolution 3(3):545-554. Abstract

Royle, J. A. and R. M. Dorazio. 2012. Parameter-expanded data augmentation for Bayesian analysis of capture-recapture models. Pages S521-S537 in Michael Schaub and William L. Kendall, editors. Proceedings EURING Analytical Conference 2009: Estimation, modelling and conservation of vertebrate populations using marked individuals. Journal of Ornithology 152(Supplement 2) Abstract

Russell, R. E., J. A. Royle, R. Desimone, M. K. Schwartz, V. L. Edwards, K. P. Pilgrim, and K. S. McKelvey. 2012. Estimating abundance of mountain lions from unstructured spatial sampling. Journal of Wildlife Management 76(8):1551-1561. Abstract

Saracco, J. F., J. A. Royle, D. F. DeSante, and B. Gardner. 2012. Spatial modeling of survival and residency and application to the Monitoring Avian Productivity and Survivorship program. Pages S469-S476 in Michael Schaub and William L. Kendall, editors. Proceedings EURING Analytical Conference 2009: Estimation, modelling and conservation of vertebrate populations using marked individuals. Journal of Ornithology 152(Supplement 2) Abstract

Sillett, T. S., R. B. Chandler, J. A. Royle, M. Kéry, and S. A. Morrison. 2012. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic. Ecological Applications 22(7):1997-2006. Abstract

Thomas, S. M., J. E. Lyons, B. A. Andres, E. E. T-Smith, E. Palacios, J. F. Cavitt, J. A. Royle, S. D. Fellows, K. Maty, W. H. Howe, E. Mellink, S. Melvin, and T. Zimmerman. 2012. Population size of snowy plovers breeding in North America. Waterbirds 35(1):1-14. Abstract

Thompson, C. M., J. A. Royle, and J. D. Garner. 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. Abstract

Yamaura, Y., J. A. Royle, N. Shimada, S. Asanuma, T. Sato, H. Taki, and S. Makino. 2012. Biodiversity of man-made open habitats in an underused country: a class of multispecies abundance models for count data. Biodiversity and Conservation 21(6):1365-1380. Abstract

2011

Bled, F., J. A. Royle, and E. Cam. 2011. Assessing hypotheses about nesting site occupancy dynamics. Ecology 92(4):938-951. Abstract

Bled, F., J. A. Royle, and E. Cam. 2011. Hierarchical modeling of an invasive spread: the Eurasian Collared-Dove Streptopelia decaocto in the United States. Ecological Applications 21(1):290-302 . Abstract

Chandler, R. B., J. A. Royle, and D. I. King. 2011. Inference about density and temporary emigration in unmarked populations. Ecology 92(7):1429-1435. Abstract

Graves, T. A., K. C. Kendall, J. A. Royle, J. B. Stetz, and A. C. Macleod. 2011. Linking landscape characteristics to local grizzly bear abundance using multiple detection methods in a hierarchical model. Animal Conservation 14(6):652-664. Abstract

Kery, M., B. Gardner, Stoeckle T., D. Weber, and J. A. Royle. 2011. Use of spatial capture-recapture modeling and DNA data to estimate densities of elusive animals. Conservation Biology 25(2):356-364. Abstract

Lyons, J. E., J. A. Royle, S. Thomas, E. Elliott-Smith, Evenson J., L. Kelly, R. Milner, and D. Nysewander. 2011. Large-scale monitoring of shorebird populations using count data and hierarchical models: Black Oystercatcher surveys by land and sea. Pages 75 in . Joint Meeting of 12th North American Crane Workshop and 34th Annual Meeting of The Waterbird Society 13-16 March, 2011 Mid-Town Holiday Inn Grand Island, NE. Final Program and Abstracts. 120 pp.

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

Martin, J., J. A. Royle, D. I. MacKenzie, H. H. Edwards, M. Kery, and B. Gardner. 2011. Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach. Methods in Ecology and Evolution 2(6):595-601. Abstract

Royle, J. A. and B. Gardner. 2011. Hierarchical spatial capture-recapture models for estimating density from trapping arrays. Pages 163-190 in Allan F. O'Connell, James D. Nichols, and K. Ullas Karanth, editors. Camera traps in animal ecology: Methods and analyses. Springer, Tokyo. xiv, 271 pp. Abstract

Royle, J. A., M. Kery, and J. Guélat. 2011. Spatial capture-recapture models for search-encounter data. Methods in Ecology and Evolution 2(6):602-611. Abstract

Royle, J. A., A. J. Magoun, B. Gardner, P. Valkenburg, and R. E. Lowell. 2011. Density estimation in a wolverine population using spatial capture-recapture models. Journal of Wildlife Management 75(3):604-611. Abstract

Yamaura, Y., J. A. Royle, K. Kuboi, T. Tada, and S. Ikeno. 2011. Modelling community dynamics based on species-level abundance models from detection/nondetection data. Journal of Applied Ecology 48(1):67-75. Abstract

Zipkin, E. F., B. Gardner, A. T. Gilbert, A. F. O'Connell, Jr., J. A. Royle, and E. D. Silverman. 2011. Distribution patterns of wintering sea ducks along the Atlantic coast in relation to local environmental characteristics and the North Atlantic oscillation. Pages 54 (abstract) in . 4th International Sea Duck Conference, Seward, Alaska, September 12-16, 2011 Program. 129 pp.

2010

Dorazio, R. M., M. Kery, J. A. Royle, and M. Plattner. 2010. Models for inference in dynamic metacommunity systems. Ecology 91(8):2466-2475. Abstract

Gardner, B., J. Reppucci, M. Lucherini, and J. A. Royle. 2010. Spatially explicit inference for open populations: estimating demographic parameters from camera-trap studies. Ecology 91(11):3376-3383. Abstract

Gardner, B., J. A. Royle, M. T. Wegan, R. E. Rainbolt, and P. D. Curtis. 2010. Estimating black bear density using DNA data from hair snares. Journal of Wildlife Management 74(2):318-325. Abstract

Griffith, E. H., J. R. Sauer, and J. A. Royle. 2010. Traffic effects on bird counts on North American Breeding Bird Survey routes. Auk 127(2):387-393. Abstract

Hines, J. E., J. D. Nichols, J. A. Royle, D. I. MacKenzie, A. M. Gopalaswamy, N. S. Kumar, and K. U. Karanth. 2010. Tigers on trails: occupancy modeling for cluster sampling. Ecological Applications 20(5):1456-1466. Abstract

Kery, M. and J. A. Royle. 2010. Hierarchical modelling and estimation of abundance and population trends in metapopulation designs. Journal of Animal Ecology 79(2):453-461. Abstract

Kery, M., J. A. Royle, H. Schmid, M. Schaub, B. Volet, G. Hafliger, and N. Zbinden. 2010. Site-occupancy distribution modeling to correct population-trend estimates derived from opportunistic observations. Conservation Biology 24(5):1388-1397. Abstract

Saracco, J. F., J. A. Royle, D. F. DeSante, and B. Gardner. 2010. Modeling spatial variation in avian survival and residency probabilities. Ecology 91(7):1885-1891. Abstract

Zipkin, E. F., B. Gardner, A. T. Gilbert, A. F. O'Connell, J. A. Royle, and E. D. Silverman. 2010. Distribution patterns of wintering sea ducks in relation to the North Atlantic Oscillation and local environmental characteristics. Oecologia 163(4):893-902. Abstract

Zipkin, E. F., J. A. Royle, D. K. Dawson, and S. Bates. 2010. Multi-species occurrence models to evaluate the effects of conservation and management actions . Biological Conservation 143(2):479-484. Abstract

2009

Forcada, J., D. Malone, J. A. Royle, and I. J. Staniland. 2009. Modelling predation by transient leopard seals for an ecosystem-based management of Southern Ocean fisheries. Ecological Modelling 220(12):1513-1521. Abstract

Franklin, M., S. Droege, D. Dawson, and J. A. Royle. 2009. Nightly and seasonal patterns of calling in common true katydids (Orthoptera: Tettigoniidae: Pterophylla camellifolia). Journal of Orthoptera Research 18(1):15-18. Abstract

Gardner, B., J. A. Royle, and M. T. Wegan. 2009. Hierarchical models for estimating density from DNA mark-recapture studies. Ecology 90(4):1106-1115. Abstract

Kery, M., R. M. Dorazio, L. Soldaat, A. van Strien, A. Zuiderwijk, and J. A. Royle. 2009. Trend estimation in populations with imperfect detection. Journal of Applied Ecology 46(6):1163-1172. Abstract

Kery, M. and J. A. Royle. 2009. Inference about species richness and community structure using species-specific occupancy models in the National Swiss Breeding Bird Survey MUB. Pages 639-656 in David L. Thomson, Evan G. Cooch, and Michael J. Conroy, editors. Modeling demographic processes in marked populations. Environmental and ecological statistics 3. Springer, New York and London. xxiv, 1136 pp. Abstract

Kery, M., J. A. Royle, M. Plattner, and R. M. Dorazio. 2009. Species richness and occupancy estimation in communities subject to temporary emigration. Ecology 90(5):1279-1290. Abstract

Royle, J. A. 2009. Analysis of capture-recapture models with individual covariates using data augmentation. Biometrics 65(1):267-274. Abstract

Royle, J. A., K. U. Karanth, A. M. Gopalaswamy, and N. S. Kumar. 2009. Bayesian inference in camera trapping studies for a class of spatial capture-recapture models. Ecology 90(11):3233-3244. Abstract

Royle, J. A., J. D. Nichols, K. U. Karanth, and A. M. Gopalaswamy. 2009. A hierarchical model for estimating density in camera-trap studies. Journal of Applied Ecology 46(1):118-127. Abstract

Russell, R. E., J. A. Royle, V. A. Saab, J. F. Lehmkuhl, W. M. Block, and J. R. Sauer. 2009. Modeling the effects of environmental disturbance on wildlife communities: avian responses to prescribed fire. Ecological Applications 19(5):1253-1263. Abstract

Weir, L., I. J. Fiske, and J. A. Royle. 2009. Trends in anuran occupancy from northeastern states of the North American Monitoring Program. Herpetological Conservation and Biology 4(3):389-402. PDF

Zipkin, E. F., A. DeWan, and J. A. Royle. 2009. Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling. Journal of Applied Ecology 46(4):815-822. Abstract

back to top

Last Updated: July 2014

Programs

Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo USA.gov logo U.S. Department of the Interior | U.S. Geological Survey
URL: http://www.pwrc.usgs.gov
Page Contact Information: Webmaster