J. Andrew Royle

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All published works

Action	Title	Year	Authors
+ PDF Chat	Integrated distance sampling models for simple point counts	2024	Marc Kéry J. Andrew Royle Tyler A. Hallman W. Douglas Robinson Nicolas Strebel Kenneth F. Kellner
+	A review of N‐mixture models	2023	Lisa Madsen J. Andrew Royle
+	Integrated distance sampling models for simple point counts	2022	Marc Kéry J. Andrew Royle Tyler A. Hallman W. Douglas Robinson Nicolas Strebel Kenneth F. Kellner
+ PDF Chat	Optimal sampling design for spatial capture–recapture	2020	Gates Dupont J. Andrew Royle Muhammad Ali Nawaz Chris Sutherland
+	Relative Abundance Models for Population Dynamics	2020	Marc Kéry J. Andrew Royle
+	Modeling Population Dynamics With Count Data	2020	Marc Kéry J. Andrew Royle
+	Dynamic N-mixture models with temporal variability in detection probability	2018	Qing Zhao J. Andrew Royle
+ PDF Chat	Adaptive Sampling for Spatial Capture-Recapture: An efficient sampling scheme for rare or patchily distributed species	2018	Alec Wong Angela K. Fuller J. Andrew Royle
+ PDF Chat	Spatial Capture-Recapture for Categorically Marked Populations with An Application to Genetic Capture-Recapture	2018	Ben C. Augustine J. Andrew Royle Sean M. Murphy Richard B. Chandler John J. Cox Marcella J. Kelly
+	Fundamental Principals of Statistical Inference	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Extensions to Basic Approaches	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Occupancy in Community-Level Studies	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	More than Two Occupancy States	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Basic Presence/Absence Situation	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Modeling Heterogeneous Detection Probabilities	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Multiple-Season Study Design	2018	Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines
+	Spatially explicit dynamic N‐mixture models	2017	Qing Zhao J. Andrew Royle G. Scott Boomer
+	Accounting for imperfect detection of groups and individuals when estimating abundance	2017	Matthew J. Clement Sarah J. Converse J. Andrew Royle
+ PDF Chat	Model‐based approaches to deal with detectability: a comment on Hutto (2016a)	2017	Tiago A. Marques Len Thomas Marc Kéry S. T. Buckland David L. Borchers Eric A. Rexstad Rachel M. Fewster Darryl I. MacKenzie J. Andrew Royle Gurutzeta Guillera‐Arroita
+ PDF Chat	A multistate dynamic site occupancy model for spatially aggregated sessile communities	2016	Keiichi Fukaya J. Andrew Royle Takehiro Okuda Masahiro Nakaoka Takashi Noda
+ PDF Chat	Estimating species – area relationships by modeling abundance and frequency subject to incomplete sampling	2016	Yuichi Yamaura Edward F. Connor J. Andrew Royle Katsuo Itoh Kiyoshi Sato Hisatomo Taki Yoshio Mishima
+	Spatial Capture-Recapture with Partial Identity: An Application to Camera Traps	2016	Ben C. Augustine J. Andrew Royle Marcella J. Kelly Christopher B. Satter Robert S. Alonso Erin E. Boydston Kevin R. Crooks
+	Estimating abundance	2016	Chris Sutherland J. Andrew Royle
+	Appendix A. Integrated likelihood and Bayesian analysis.	2016	J. Andrew Royle Marc Kéry Roland Gautier Hans Schmid
+	Appendix B. Estimates of alpha (the treatment effect) with random effects (i.e., the borrowing of information from other species) and without random effects.	2016	Robin E. Russell J. Andrew Royle Victoria A. Saab John F. Lehmkuhl William M. Block John R. Sauer
+	Appendix A. Details for computing the marginal likelihood and obtaining the maximum likelihood estimators.	2016	J. Andrew Royle Richard B. Chandler Kimberly D. Gazenski Tabitha A. Graves
+	Appendix C. Model implementation details and JAGS code for the northern dusky salamander model.	2016	Elise F. Zipkin James T. Thorson Kevin E. See Heather J. Lynch Evan H. Campbell Grant Yoichiro Kanno Richard B. Chandler Benjamin H. Letcher J. Andrew Royle
+	Appendix C. Simulation results comparing maximum-likelihood estimates with those obtained using the Markov chain Monte Carlo method.	2016	James E. Hines James D. Nichols J. Andrew Royle Darryl I. MacKenzie Arjun M. Gopalaswamy N. Samba Kumar K. Ullas Karanth
+	Supplement 2. Evaluation of the approximation of the detection function and alternative implementations.	2016	Rahel Sollmann Beth Gardner Richard B. Chandler J. Andrew Royle T. Scott Sillett
+	Appendix C. Details of the simulation study of the Jolly-Seber extension to our spatially explicit capture–recapture model.	2016	Beth Gardner Juan I. Reppucci Mauro Lucherini J. Andrew Royle
+	Appendix C. Simulation results for parameters associated with abundance and detection from Markov data analyzed with the Markov and log-linear trend models.	2016	Rahel Sollmann Beth Gardner Richard B. Chandler J. Andrew Royle T. Scott Sillett
+	Modeling Abundance with Counts of Unmarked Individuals in Closed Populations	2015	Marc Kéry J. Andrew Royle
+	Modeling Abundance Using Hierarchical Distance Sampling	2015	Marc Kéry J. Andrew Royle
+	Advanced Hierarchical Distance Sampling	2015	Marc Kéry J. Andrew Royle
+	What Are Hierarchical Models and How Do We Analyze Them?	2015	Marc Kéry J. Andrew Royle
+	Modeling Abundance Using Multinomial N-Mixture Models	2015	Marc Kéry J. Andrew Royle
+	Fitting Models Using the Bayesian Modeling Software BUGS and JAGS	2015	Marc Kéry J. Andrew Royle
+	Linear Models, Generalized Linear Models (GLMs), and Random Effects Models	2015	Marc Kéry J. Andrew Royle
+ PDF Chat	Correction: Trap Configuration and Spacing Influences Parameter Estimates in Spatial Capture-Recapture Models	2015	Catherine Sun Angela K. Fuller J. Andrew Royle
+	Spatial Capture-recapture with Partial Identity	2015	J. Andrew Royle
+	Rachel S. McCrea and Byron J. T. Morgan, Analysis of Capture–Recapture Data	2015	J. Andrew Royle
+ PDF Chat	Likelihood analysis of spatial capture‐recapture models for stratified or class structured populations	2015	J. Andrew Royle Chris Sutherland Angela K. Fuller Catherine Sun
+	Spatial Capture-recapture with Partial Identity	2015	J. Andrew Royle
+ PDF Chat	An open‐population hierarchical distance sampling model	2014	Rahel Sollmann Beth Gardner Richard B. Chandler J. Andrew Royle T. Scott Sillett
+	Reply to Efford on <i>‘Integrating resource selection information with spatial capture–recapture’</i>	2014	J. Andrew Royle Richard B. Chandler Catherine Sun Angela K. Fuller
+ PDF Chat	Trap Configuration and Spacing Influences Parameter Estimates in Spatial Capture-Recapture Models	2014	Catherine Sun Angela K. Fuller J. Andrew Royle
+ PDF Chat	Inferences about population dynamics from count data using multistate models: a comparison to capture–recapture approaches	2014	Elise F. Zipkin T. Scott Sillett Evan H. Campbell Grant Richard B. Chandler J. Andrew Royle
+ PDF Chat	Modeling Trends from North American Breeding Bird Survey Data: A Spatially Explicit Approach	2013	Florent Bled John R. Sauer Keith L. Pardieck Paul F. Doherty J. Andrew Royle
+ PDF Chat	Hierarchical spatial capture–recapture models: modelling population density in stratified populations	2013	J. Andrew Royle Sarah J. Converse
+	Spatial Capture-Recapture	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Developing Markov Chain Monte Carlo Samplers	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Spatial Mark-Resight Models	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	GLMs and Bayesian Analysis	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Modeling Variation in Encounter Probability	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Stratified Populations: Multi-Session and Multi-Site Data	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Open Population Models	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner
+	Population abundance, size structure and sex-ratio in an insular lizard	2013	Simone Tenan Andreu Rotger José Manuel Igual Óscar Moya J. Andrew Royle Giacomo Tavecchia
+	Spatially explicit models for inference about density in unmarked or partially marked populations	2013	Richard B. Chandler J. Andrew Royle
+	Review of: Mixed Effects Models and Extensions in Ecology with R	2013	J. Andrew Royle
+ PDF Chat	Integrating resource selection information with spatial capture–recapture	2013	J. Andrew Royle Richard B. Chandler Catherine Sun Angela K. Fuller
+	Integrating Resource Selection Information with Spatial Capture-Recapture	2012	J. Andrew Royle Richard B. Chandler
+	Data Augmentation for Hierarchical Capture-recapture Models	2012	J. Andrew Royle Sarah J. Converse William A. Link
+	Assessment of bias in US waterfowl harvest estimates	2012	Paul I. Padding J. Andrew Royle
+	Integrating Resource Selection Information with Spatial Capture-Recapture	2012	J. Andrew Royle Richard B. Chandler
+ PDF Chat	Inference about density and temporary emigration in unmarked populations	2011	Richard B. Chandler J. Andrew Royle David I. King
+	Parameter-expanded data augmentation for Bayesian analysis of capture–recapture models	2010	J. Andrew Royle Robert M. Dorazio
+	Hierarchical Spatial Capture–Recapture Models for Estimating Density from Trapping Arrays	2010	J. Andrew Royle
+	A hierarchical model for spatial capture–recapture data: comment	2010	Tiago A. Marques Len Thomas J. Andrew Royle
+	Estimating Black Bear Density Using DNA Data From Hair Snares	2010	Beth Gardner J. Andrew Royle Michael T. Wegan Raymond E. Rainbolt Paul D. Curtis
+	Tigers on Trails: Occupancy Modeling for Cluster Sampling	2009	James E. Hines James Hastings Nichols J. Andrew Royle Darryl I. MacKenzie Arjun M. Gopalaswamy Samba Kumar Krithi K. Karanth
+ PDF Chat	Hierarchical modelling and estimation of abundance and population trends in metapopulation designs	2009	Marc Kéry J. Andrew Royle
+	Bayesian inference in camera trapping studies for a class of spatial capture–recapture models	2009	J. Andrew Royle K. Ullas Karanth Arjun M. Gopalaswamy N. Samba Kumar
+	Hierarchical models for estimating density from DNA mark–recapture studies	2009	Beth Gardner J. Andrew Royle Michael T. Wegan
+	A Double‐Observer Method to Estimate Detection Rate During Aerial Waterfowl Surveys	2008	Mark D. Koneff J. Andrew Royle Mark C. Otto JAMES S. WORTHAM JOHN K. BIDWELL
+	A HIERARCHICAL MODEL FOR SPATIAL CAPTURE–RECAPTURE DATA	2008	J. Andrew Royle Kevin V. Young
+	Analysis of Capture–Recapture Models with Individual Covariates Using Data Augmentation	2008	J. Andrew Royle
+	Hierarchical modeling of cluster size in wildlife surveys	2008	J. Andrew Royle
+	Making Great Leaps Forward: Accounting for Detectability in Herpetological Field Studies	2007	Marc J. Mazerolle Larissa L. Bailey William L. Kendall J. Andrew Royle Sarah J. Converse James D. Nichols
+	Modeling Individual Effects in the Cormack–Jolly–Seber Model: A State–Space Formulation	2007	J. Andrew Royle
+	Analysis of Multinomial Models With Unknown Index Using Data Augmentation	2007	J. Andrew Royle Robert M. Dorazio William A. Link
+	GENERALIZED SITE OCCUPANCY MODELS ALLOWING FOR FALSE POSITIVE AND FALSE NEGATIVE ERRORS	2006	J. Andrew Royle William A. Link
+	Site Occupancy Models with Heterogeneous Detection Probabilities	2005	J. Andrew Royle
+	A GENERAL CLASS OF MULTINOMIAL MIXTURE MODELS FOR ANURAN CALLING SURVEY DATA	2005	J. Andrew Royle William A. Link
+	Rejoinder to "The Performance of Mixture Models in Heterogeneous Closed Population Capture‐Recapture"	2005	Robert M. Dorazio J. Andrew Royle
+	Dynamic design of ecological monitoring networks for non‐Gaussian spatio‐temporal data	2005	Christopher K. Wikle J. Andrew Royle
+	Estimating Size and Composition of Biological Communities by Modeling the Occurrence of Species	2005	Robert M. Dorazio J. Andrew Royle
+	MODELING ABUNDANCE EFFECTS IN DISTANCE SAMPLING	2004	J. Andrew Royle Dana Dawson Scott C. Bates
+ PDF Chat	<i>N</i>‐Mixture Models for Estimating Population Size from Spatially Replicated Counts	2004	J. Andrew Royle
+	Demographic Analysis from Summaries of an Age‐Structured Population	2003	William A. Link J. Andrew Royle Jeff S. Hatfield
+	Mixture Models for Estimating the Size of a Closed Population When Capture Rates Vary among Individuals	2003	Robert M. Dorazio J. Andrew Royle
+	ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE	2002	Darryl I. MacKenzie James D. Nichols Gideon B. Lachman Sam Droege J. Andrew Royle Catherine A. Langtimm
+	Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One	2002	Darryl I. MacKenzie James D. Nichols Gideon B. Lachman Sam Droege J. Andrew Royle Catherine A. Langtimm
+	Random effects and shrinkage estimation in capture-recapture models	2002	J. Andrew Royle William A. Link

Common Coauthors

Coauthor	Papers Together
Richard B. Chandler	20
Marc Kéry	14
Darryl I. MacKenzie	12
James D. Nichols	11
Rahel Sollmann	10
James E. Hines	9
Larissa L. Bailey	8
Beth Gardner	7
Kenneth H. Pollock	7
William A. Link	6
Angela K. Fuller	6
Beth Gardner	6
Catherine Sun	5
Robert M. Dorazio	5
Sarah J. Converse	4
T. Scott Sillett	4
Chris Sutherland	3
Arjun M. Gopalaswamy	3
Tiago A. Marques	2
Michael T. Wegan	2
Sam Droege	2
John R. Sauer	2
Kenneth F. Kellner	2
Evan H. Campbell Grant	2
Ben C. Augustine	2
Qing Zhao	2
Elise F. Zipkin	2
Nicolas Strebel	2
W. Douglas Robinson	2
Tyler A. Hallman	2
Len Thomas	2
Gideon B. Lachman	2
Catherine A. Langtimm	2
N. Samba Kumar	2
Marcella J. Kelly	2
Masahiro Nakaoka	1
Kevin R. Crooks	1
Jeff S. Hatfield	1
William L. Kendall	1
Colleen M. Handel	1
James T. Thorson	1
John F. Lehmkuhl	1
Paul F. Doherty	1
Yuichi Yamaura	1
JOHN K. BIDWELL	1
Gates Dupont	1
Mark D. Koneff	1
Eric A. Rexstad	1
Yoichiro Kanno	1
Lisa Madsen	1

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	<i>N</i>‐Mixture Models for Estimating Population Size from Spatially Replicated Counts	2004	J. Andrew Royle	21
+	Mixture Models for Estimating the Size of a Closed Population When Capture Rates Vary among Individuals	2003	Robert M. Dorazio J. Andrew Royle	18
+ PDF Chat	Density estimation in live‐trapping studies	2004	Murray G. Efford	18
+	Spatially Explicit Maximum Likelihood Methods for Capture–Recapture Studies	2007	David L. Borchers Murray G. Efford	16
+	Analysis of Multinomial Models With Unknown Index Using Data Augmentation	2007	J. Andrew Royle Robert M. Dorazio William A. Link	16
+	A HIERARCHICAL MODEL FOR SPATIAL CAPTURE–RECAPTURE DATA	2008	J. Andrew Royle Kevin V. Young	15
+	ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE	2002	Darryl I. MacKenzie James D. Nichols Gideon B. Lachman Sam Droege J. Andrew Royle Catherine A. Langtimm	14
+	The Use of Mixed Logit Models to Reflect Heterogeneity in Capture‐Recapture Studies	1999	Brent A. Coull Alan Agresti	14
+	Nonidentifiability of Population Size from Capture‐Recapture Data with Heterogeneous Detection Probabilities	2003	William A. Link	12
+	Nonparametric MLE under Two Closed Capture-Recapture Models with Heterogeneity	1996	James L. Norris Kenneth H. Pollock	11
+	Analysis of Capture–Recapture Models with Individual Covariates Using Data Augmentation	2008	J. Andrew Royle	11
+	Logistic Regression in Capture-Recapture Models	1990	Juha M. Alho	10
+ PDF Chat	Unified Maximum Likelihood Estimates for Closed Capture–Recapture Models Using Mixtures	2000	Shirley Pledger	10
+	On the statistical analysis of capture experiments	1989	Richard Huggins	10
+	Site Occupancy Models with Heterogeneous Detection Probabilities	2005	J. Andrew Royle	9
+	ESTIMATING TEMPORARY EMIGRATION USING CAPTURE–RECAPTURE DATA WITH POLLOCK’S ROBUST DESIGN	1997	William L. Kendall James D. Nichols James E. Hines	9
+	Estimation of the size of a closed population when capture probabilities vary among animals	1978	Kenneth P. Burnham W. Scott Overton	8
+	A Capture-Recapture Design Robust to Unequal Probability of Capture	1982	Kenneth H. Pollock	8
+	JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling	2003	Martyn Plummer	8
+	MODELING ABUNDANCE EFFECTS IN DISTANCE SAMPLING	2004	J. Andrew Royle Dana Dawson Scott C. Bates	8
+	Introduction to Distance Sampling: Estimating Abundance of Biological Populations	2001	S. T. Buckland Debra Anderson K. P. Burnham Jeff Laake David L. Borchers Len Thomas	7
+	Spatial Capture-Recapture	2013	J. Andrew Royle Richard B. Chandler Rahel Sollmann Beth Gardner	7
+	ROBUSTNESS OF CLOSED CAPTURE–RECAPTURE METHODS TO VIOLATIONS OF THE CLOSURE ASSUMPTION	1999	William L. Kendall	7
+	Bayesian inference in camera trapping studies for a class of spatial capture–recapture models	2009	J. Andrew Royle K. Ullas Karanth Arjun M. Gopalaswamy N. Samba Kumar	7
+	Models for Estimating Abundance from Repeated Counts of an Open Metapopulation	2010	D. B. Dail Lisa Madsen	7
+	Modeling Survival and Testing Biological Hypotheses Using Marked Animals: A Unified Approach with Case Studies	1992	Jean‐Dominique Lebreton Kenneth P. Burnham Jean Clobert David R. Anderson	7
+ PDF Chat	A DOUBLE-OBSERVER APPROACH FOR ESTIMATING DETECTION PROBABILITY AND ABUNDANCE FROM POINT COUNTS	2000	James D. Nichols James E. Hines John R. Sauer F. W. Fallon Jane E. Fallon Patricia J. Heglund	6
+ PDF Chat	Classical Multilevel and Bayesian Approaches to Population Size Estimation Using Multiple Lists	1999	Stephen E. Fienberg Matthew Johnson Brain W. Junker	6
+	Parameter-expanded data augmentation for Bayesian analysis of capture–recapture models	2010	J. Andrew Royle Robert M. Dorazio	6
+	Statistical Inference for Capture-Recapture Experiments.	1992	A Lawson Kenneth H. Pollock James D. Nichols Cavell Brownie James E. Hines	6
+ PDF Chat	Estimating the Size of a Multinomial Population	1972	Lalitha Sanathanan	6
+ PDF Chat	Program MARK: survival estimation from populations of marked animals	1999	Gary C. White Kenneth P. Burnham	6
+	Estimating Size and Composition of Biological Communities by Modeling the Occurrence of Species	2005	Robert M. Dorazio J. Andrew Royle	5
+ PDF Chat	A non-technical overview of spatially explicit capture–recapture models	2010	David L. Borchers	5
+ PDF Chat	General Methods for Monitoring Convergence of Iterative Simulations	1998	Stephen P. Brooks Andrew Gelman	5
+	Estimating Black Bear Density Using DNA Data From Hair Snares	2010	Beth Gardner J. Andrew Royle Michael T. Wegan Raymond E. Rainbolt Paul D. Curtis	5
+	A General Methodology for the Analysis of Capture-Recapture Experiments in Open Populations	1996	Carl J. Schwarz A. Neil Arnason	5
+	Improving Removal‐Based Estimates of Abundance by Sampling a Population of Spatially Distinct Subpopulations	2005	Robert M. Dorazio Howard L. Jelks Frank Jordan	5
+	The Calculation of Posterior Distributions by Data Augmentation	1987	Martin A. Tanner Wing Hung Wong	5
+	POSTERIOR PREDICTIVE ASSESSMENT OF MODEL FITNESS VIA REALIZED DISCREPANCIES	1996	Andrew Gelman Xiao‐Li Meng Hal S. Stern	4
+ PDF Chat	Spatial Capture-Recapture	2014	Edward O. Garton	4
+	Simple Capture-Recapture Models Permitting Unequal Catchability and Variable Sampling Effort	1994	Alan Agresti	4
+	Modeling Individual Effects in the Cormack–Jolly–Seber Model: A State–Space Formulation	2007	J. Andrew Royle	4
+ PDF Chat	The Use of Auxiliary Variables in Capture-Recapture and Removal Experiments	1984	Kenneth H. Pollock James E. Hines James D. Nichols	4
+ PDF Chat	Inference about density and temporary emigration in unmarked populations	2011	Richard B. Chandler J. Andrew Royle David I. King	4
+	The Performance of Mixture Models in Heterogeneous Closed Population Capture–Recapture	2005	Shirley Pledger	4
+ PDF Chat	Inference from Iterative Simulation Using Multiple Sequences	1992	Andrew Gelman Donald B. Rubin	4
+	Open Capture‐Recapture Models with Heterogeneity: I. Cormack‐Jolly‐Seber Model	2003	Shirley Pledger Kenneth H. Pollock James L. Norris	4
+ PDF Chat	SMALL-MAMMAL DENSITY ESTIMATION: A FIELD COMPARISON OF GRID-BASED VS. WEB-BASED DENSITY ESTIMATORS	2003	Robert Parmenter Terry L. Yates David R. Anderson Kenneth P. Burnham Jonathan L. Dunnum Alan B. Franklin Michael T. Friggens Bruce C. Lubow Michael T. Miller Gail S. Olson	4
+	The use of auxiliary variables in capture-recapture modelling: An overview	2002	Kenneth H. Pollock	4