J. andrew Royle

J. andrew Royle
United States Geological Survey | USGS · Patuxent Wildlife Research Center

PhD Statistics

About

336
Publications
109,270
Reads
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27,077
Citations
Additional affiliations
June 2004 - present
United States Geological Survey
Position
  • Research Statistician

Publications

Publications (336)
Article
Full-text available
Spatial capture–recapture (SCR) models are a relatively recent development in quantitative ecology, and they are becoming widely used to model density in studies of animal populations using camera traps, DNA sampling and other methods which produce spatially explicit individual encounter information. One of the core assumptions of SCR models is tha...
Article
Full-text available
Conservation and management of spatially structured populations is challenging because solutions must consider where individuals are located, but also differential individual space use as a result of landscape heterogeneity. A recent extension of spatial capture-recapture (SCR) models, the ecological distance model, uses spatial encounter histories...
Article
Full-text available
Spatial heterogeneity in the environment induces variation in population demographic rates and dispersal patterns, which result in spatio-temporal variation in density and gene flow. Unfortunately, applying theory to learn about the role of spatial structure on populations has been hindered by the lack of mechanistic spatial models and inability to...
Article
Full-text available
Acoustic sampling methods are becoming increasingly important in biological monitoring. Sound attenuation is one of the most important dynamics affecting the utility of bioacoustic data as it directly affects the probability of detection of individuals from bioacoustic arrays and especially the localization of acoustic signals necessary in telemetr...
Article
Full-text available
Acoustic surveys of vocalizing animals are conducted to determine density, distribution, and diversity. Acoustic surveys are traditionally performed by human listeners, but automated recording devices (ARD) are becoming increasingly popular. Signal strength decays, or attenuates, with increasing distance between source and receiver and some habitat...
Article
Full-text available
Species-specific population estimates are fundamental for many aspects of ecology, evolution, and conservation, yet they are lacking for most species. Aiming to fill this gap, Callaghan et al. (1) estimated global bird population sizes by modeling the relationship between eBird reporting rates and independent estimates and extrapolating globally. W...
Article
The COVID-19 pandemic has disrupted field research programs, making conservation and management decision-making more challenging. However, it may be possible to conduct population assessments using integrated models that combine community science data with existing data from structured surveys. We developed a space-time integrated model to characte...
Article
Full-text available
The management of North American waterfowl is predicated on long‐term, continental scale banding implemented prior to the hunting season (i.e., July–September) and subsequent reporting of bands recovered by hunters. However, single‐season banding and encounter operations have a number of characteristics that limit their application to estimating de...
Article
Full-text available
1. Spatial capture-recapture (SCR) models have increasingly been used as a basis for combining capture-recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are availab...
Article
Full-text available
Spatial capture‐recapture (SCR) has emerged as the industry standard for estimating population density by leveraging information from spatial locations of repeat encounters of individuals. The precision of density estimates depends fundamentally on the number and spatial configuration of traps. Despite this knowledge, existing sampling design recom...
Article
Full-text available
The ongoing recovery of terrestrial large carnivores in North America and Europe is accompanied by intense controversy. On the one hand, reestablishment of large carnivores entails a recovery of their most important ecological role, predation. On the other hand, societies are struggling to relearn how to live with apex predators that kill livestock...
Article
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Accelerating declines of an increasing number of animal populations worldwide necessitate methods to reliably and efficiently estimate demographic parameters such as population density and trajectory. Standard methods for estimating demographic parameters from noninvasive genetic samples are inefficient because lower-quality samples cannot be used,...
Article
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Background: Acoustic telemetry technologies are being increasingly deployed to study a variety of aquatic taxa including fishes, reptiles, and marine mammals. Large cooperative telemetry networks produce vast quantities of data useful in the study of movement, resource selection and species distribution. Efficient use of acoustic telemetry data re...
Article
Full-text available
Over the past half century, migratory birds in North America have shown divergent population trends relative to resident species, with the former declining rapidly and the latter increasing. The role that climate change has played in these observed trends is not well understood, despite significant warming over this period. We used 43 y of monitori...
Preprint
Full-text available
Spatial capture-recapture (SCR) has emerged as the industry standard for analyzing observational data to estimate population size by leveraging information from spatial locations of repeat encounters of individuals. The resulting precision of density estimates depends fundamentally on the number and spatial configuration of traps. Despite this know...
Article
Full-text available
Many models in population ecology, including spatial capture–recapture (SCR) models, assume that individuals are distributed and detected independently of one another. In reality, this is rarely the case – both antagonistic and gregarious relationships lead to non-independent spatial configurations, with territorial exclusion at one end of the spec...
Article
Full-text available
There is considerable interest in evaluating the status and trends of sturgeon populations, yet many traditional approaches to estimating the abundance of fishes are intractable due to their biology and rarity. Side-scan sonar has recently emerged as an effective tool for censusing sturgeon in rivers, yet challenges remain for censusing open popula...
Preprint
Full-text available
Accelerating declines of an increasing number of animal populations worldwide necessitate methods to reliably and efficiently estimate demographic parameters such as population density and trajectory. Standard methods for estimating demographic parameters from noninvasive genetic samples are inefficient because lower quality samples cannot be used,...
Preprint
Full-text available
Background: Acoustic telemetry technologies are being rapidly deployed to study a variety of aquatic taxa including fishes, reptiles, and marine mammals. Large cooperative telemetry networks produce vast quantities of data useful in the study of movement, resource selection and species distribution. Efficient use of acoustic telemetry data requires...
Article
Full-text available
Trends in population abundance can be challenging to quantify during range expansion and contraction, when there is spatial variation in trend, or the conservation area is large. We used genetic detection data from natural bear rubbing sites and spatial capture-recapture (SCR) modeling to estimate local density and population growth rates in a griz...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Species distributions are determined by the interaction of multiple biotic and abiotic factors, which produces complex spatial and temporal patterns of occurrence. As habitats and climate change due to anthropogenic activities, there is a need to develop species distribution models that can quantify these complex range dynamics. In this paper, we d...
Article
Full-text available
Information about population abundance, distribution, and demographic rates are critical for understanding a species’ ecology and for effective conservation and management. To collect data over large spatial and temporal extents for such inferences, especially for species with low densities or wide distributions, citizen science can be an efficient...
Article
Ecological distance-based spatial capture-recapture models (SCR) are a promising approach for simultaneously estimating animal density and connectivity, both of which affect spatial population processes and ultimately species persistence. We explored how SCR models can be integrated into reserve-design frameworks that explicitly acknowledge both th...
Article
Full-text available
Spatial capture‐recapture (SCR) methods have become widely applied in ecology. The immediate adoption of SCR is due to the fact that it resolves some major criticisms of traditional capture‐recapture methods related to heterogeneity in detectabililty, and the emergence of new technologies (e.g., camera traps, non‐invasive genetics) has vastly impro...
Article
Full-text available
Climate change has been identified as one of the most important drivers of wildlife population dynamics. The in‐depth knowledge of the complex relationships between climate and population sizes through density dependent demographic processes is important for understanding and predicting population shifts under climate change, which requires integra...
Article
Full-text available
Recently introduced unmarked spatial capture–recapture (SCR), spatial mark–resight (SMR), and 2‐flank spatial partial identity models (SPIMs) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can re...
Article
Full-text available
The Anthropocene is an era of marked human impact on the world. Quantifying these impacts has become central to understanding the dynamics of coupled human‐natural systems, resource‐dependent livelihoods, and biodiversity conservation. Ecologists are facing growing pressure to quantify the size, distribution, and trajectory of wild populations in a...
Article
In theory parameters of dynamic N-mixture models can be estimated with multiple years of data without the robust design under the assumption of constant detection probability. However, such an assumption can rarely be met in long-term studies, and the consequences of violating this assumption in the inferences of dynamic N-mixture models have not b...
Article
Full-text available
We present the first regional trends in anuran occupancy for eight states of the southeastern United States, based on 13 y (2001-2013) of North American Amphibian Monitoring Program (NAAMP) data. The NAAMP is a long-term monitoring program in which observers collect anuran calling observation data at fixed locations along random roadside routes. We...
Data
Complete dataset including transect #, temperature, wind speed, humidity, barometric pressure, ambient noise, line of sight, visible (detection or non detection), species, habitat, and distance.
Data
Playback file consisting of four pure tones at 1, 3, 5, and 7 kHz, six anuran calls, and six birds calls. The anuran calls used were the wood frog (Rana [Lithobates] sylvaticus), California red-legged frog (Rana [Lithobates] draytonii), Houston toad (Bufo [Anaxyrus] houstonensis), Arroyo toad (Bufo [Anaxyrus] californicus), American bullfrog (Rana...
Data
Supplementary information including summary statistics for all playback audio, individual graphs of detection probability by distance for each habitat and species combination with 95% confidence intervals, and a complete summary of the top statistical model.
Data
R code including model description, model selection, predicting detection probability, and generating figures.
Article
Full-text available
Emerging infectious pathogens are responsible for some of the most severe host mass mortality events in wild populations. Yet, effective pathogen control strategies are notoriously difficult to identify, in part because quantifying and forecasting pathogen spread and disease dynamics is challenging. Following an outbreak, hosts must cope with the p...
Article
Worldwide, private lands have attracted increased attention from conservationists, not only because most of the globe is privately owned, but also because private lands can be an asset to the protected area conservation strategy. In Brazil, the riverine Areas of Permanent Protection (APPs) are a key instrument of the Forest Code to protect biodiver...
Preprint
Full-text available
Rare species present challenges to data collection, particularly when the species is spatially clustered over large areas, such that the encounter frequency of the organism is low. Sampling where the organism is absent consumes resources, and offers relatively low-quality information which are often difficult to model using standard statistical met...
Article
1.Acoustic sampling methods are becoming increasingly important in biological monitoring. Sound attenuation is one of the most important dynamics affecting the utility of acoustic data as it directly affects the probability of detection of individuals by acoustic sensor arrays and especially the localization of acoustic signals necessary in telemet...
Article
Full-text available
Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representative spatial scales that are insensitive to local heterogeneity is challenging. We examine the link between polyc...
Article
Full-text available
1.Spatial capture‐recapture (SCR) models are commonly used for analyzing data collected using non‐invasive genetic sampling (NGS). Opportunistic NGS often leads to detections that do not occur at discrete detector locations. Therefore, spatial aggregation of individual detections into fixed detectors (e.g. center of grid cells) is an option to incr...
Preprint
Full-text available
The estimation of animal population density is a fundamental goal in wildlife ecology and management, commonly met using mark recapture or spatial mark recapture (SCR) study designs and statistical methods. Mark-recapture methods require the identification of individuals ; however, for many species and sampling methods, particularly noninvasive met...
Article
Full-text available
Camera trapping surveys frequently capture individuals whose identity is only known from a single flank. The most widely used methods for incorporating these partial identity individuals into density analyses discard some of the partial identity capture histories, reducing precision, and while not previously recognized, introducing bias. Here, we p...
Preprint
Full-text available
Recently introduced unmarked spatial capture-recapture (SCR), spatial mark-resight (SMR), and 2-flank spatial partial identity models (SPIM) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can rel...
Article
Sporadic sightings of the endangered Amur tiger Panthera tigris altaica along the China-Russia border during the late 1990s sparked efforts to expand this subspecies distribution and abundance by restoring potentially suitable habitats in the Changbai Mountains. To guide science-based recovery efforts and provide a baseline for future monitoring of...
Article
Full-text available
Recent developments of community abundance models (CAMs) enable us to analyze communities subject to imperfect detection. However, existing CAMs assume spatial closure, that is, that individuals are always present in the sampling plots, which is often violated in field surveys. Violation of this assumption, such as in the presence of spatial tempor...
Book
Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition, provides a synthesis of model-based approaches for analyzing presence-absence data, allowing for imperfect detection. Beginning from the relatively simple case of estimating the proportion of area or sampling units occupied at the time of surve...
Chapter
Capture-recapture can be viewed as an animal survey method in which the count statistic is the total number of animals caught, and the associated detection probability is the probability of capture.
Chapter
Tigers predominantly prey on large ungulate species, such as sambar (Cervus unicolor), red deer (Cervus elaphus), gaur (Bos gaurus), banteng (Bos javanicus), chital (Axis axis), muntjac (Muntiacus muntjak), wild pig (Sus scrofa), and bearded pig (Sus barbatus). The density of a tiger population is strongly correlated with the density of such prey s...
Article
Knowledge of demographic parameters such as survival, reproduction, emigration, and immigration is essential to understand metapopulation dynamics. Traditionally the estimation of these demographic parameters requires intensive data from marked animals. The development of dynamic N-mixture models makes it possible to estimate demographic parameters...
Article
Full-text available
Vague and/or ad hoc definitions of the area sampled in monitoring efforts are common, and estimates of ecological state variables (e.g. distribution and abundance) can be sensitive to such specifications. The uncertainty in population metrics due to data deficiencies, vague definitions of space and lack of standardized protocols is a major challeng...
Article
Full-text available
If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities <1. Common estimators include double-observer models, distance sampling models and combined double-observer and distance sampling models (known as mark-recapture-distance-sampling models; MRDS). When animals resid...
Article
Full-text available
The Andean bear (Tremarctos ornatus) is the only extant species of bear in South America and is considered threatened across its range and endangered in Ecuador. Habitat loss and fragmentation is considered a critical threat to the species, and there is a lack of knowledge regarding its distribution and abundance. The species is thought to occur at...
Preprint
Full-text available
Camera trapping surveys frequently capture individuals whose identity is only known from a single flank. The most widely used methods for incorporating these partial identity individuals into density analyses discard some of the partial identity capture histories, reducing precision, and while not previously recognized, introducing bias. Here, we p...
Article
Full-text available
In a recent paper, Hutto (2016a) challenges the need to account for detectability when interpreting data from point counts. A number of issues with model-based approaches to deal with detectability are presented, and an alternative suggested: surveying an area around each point over which detectability is assumed certain. The article contains a num...