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J. Andrew Royle

Publications and source records attributed to J. Andrew Royle.

At least 163 records · Page 9Linked to original sources

A hierarchical model for estimating density in camera-trap studies

Estimating animal density using capture–recapture data from arrays of detection devices such as camera traps has been problematic due to the movement of individuals and heterogeneity in capture probability among them induced by differential exposure to trapping. We develop a spatial capture–recapture model for estimating density from camera-trapping data which contains explicit models for the spatial point process governing the distribution of individuals and their exposure to and detection by traps. We adopt a Bayesian approach to analysis of the hierarchical model using the technique of data augmentation. The model is applied to photographic capture–recapture data on tigers Panthera tigris in Nagarahole reserve, India. Using this model, we estimate the density of tigers to be 14·3 animals per 100 km 2 during 2004. Synthesis and applications. Our modelling framework largely overcomes several weaknesses in conventional approaches to the estimation of animal density from trap arrays. It effectively deals with key problems such as individual heterogeneity in capture probabilities, movement of traps, presence of potential ‘holes’ in the array and ad hoc estimation of sample area. The formulation, thus, greatly enhances flexibility in the conduct of field surveys as well as in the analysis of data, from studies that may involve physical, photographic or DNA-based ‘captures’ of individual animals.

Journal of Applied Ecology

Modelling predation by transient leopard seals for an ecosystem-based management of Southern Ocean fisheries

Correctly quantifying the impacts of rare apex marine predators is essential to ecosystem-based approaches to fisheries management, where harvesting must be sustainable for targeted species and their dependent predators. This requires modelling the uncertainty in such processes as predator life history, seasonal abundance and movement, size-based predation, energetic requirements, and prey vulnerability. We combined these uncertainties to evaluate the predatory impact of transient leopard seals on a community of mesopredators (seals and penguins) and their prey at South Georgia, and assess the implications for an ecosystem-based management. The mesopredators are highly dependent on Antarctic krill and icefish, which are targeted by regional fisheries. We used a state-space formulation to combine (1) a mark-recapture open-population model and individual identification data to assess seasonally variable leopard seal arrival and departure dates, numbers, and residency times; (2) a size-based bioenergetic model; and (3) a size-based prey choice model from a diet analysis. Our models indicated that prey choice and consumption reflected seasonal changes in leopard seal population size and structure, size-selective predation and prey vulnerability. A population of 104 (90-125) leopard seals, of which 64% were juveniles, consumed less than 2% of the Antarctic fur seal pup production of the area (50% of total ingested energy, IE), but ca. 12-16% of the local gentoo penguin population (20% IE). Antarctic krill (28% IE) were the only observed food of leopard seal pups and supplemented the diet of older individuals. Direct impacts on krill and fish were negligible, but the "escapement" due to leopard seal predation on fur seal pups and penguins could be significant for the mackerel icefish fishery at South Georgia. These results suggest that: (1) rare apex predators like leopard seals may control, and may depend on, populations of mesopredators dependent on prey species targeted by fisheries; and (2) predatory impacts and community control may vary throughout the predator's geographic range, and differ across ecosystems and management areas, depending on the seasonal abundance of the prey and the predator's dispersal movements. This understanding is important to integrate the predator needs as natural mortality of its prey in models to set prey catch limits for fisheries. Reliable estimates of the variability of these needs are essential for a precautionary interpretation in the context of an ecosystem-based management. ?? 2009 Elsevier B.V.

Ecological Modelling

Impacts of forest fragmentation on species richness: A hierarchical approach to community modelling

1. Species richness is often used as a tool for prioritizing conservation action. One method for predicting richness and other summaries of community structure is to develop species-specific models of occurrence probability based on habitat or landscape characteristics. However, this approach can be challenging for rare or elusive species for which survey data are often sparse. 2. Recent developments have allowed for improved inference about community structure based on species-specific models of occurrence probability, integrated within a hierarchical modelling framework. This framework offers advantages to inference about species richness over typical approaches by accounting for both species-level effects and the aggregated effects of landscape composition on a community as a whole, thus leading to increased precision in estimates of species richness by improving occupancy estimates for all species, including those that were observed infrequently. 3. We developed a hierarchical model to assess the community response of breeding birds in the Hudson River Valley, New York, to habitat fragmentation and analysed the model using a Bayesian approach. 4. The model was designed to estimate species-specific occurrence and the effects of fragment area and edge (as measured through the perimeter and the perimeter/area ratio, P/A), while accounting for imperfect detection of species. 5. We used the fitted model to make predictions of species richness within forest fragments of variable morphology. The model revealed that species richness of the observed bird community was maximized in small forest fragments with a high P/A. However, the number of forest interior species, a subset of the community with high conservation value, was maximized in large fragments with low P/A. 6. Synthesis and applications. Our results demonstrate the importance of understanding the responses of both individual, and groups of species, to environmental heterogeneity while illustrating the utility of hierarchical models for inference about species richness for conservation. This framework can be used to investigate the impacts of land-use change and fragmentation on species or assemblage richness, and to further understand trade-offs in species-specific occupancy probabilities associated with landscape variability.

New York

Species richness and occupancy estimation in communities subject to temporary emigration

Species richness is the most common biodiversity metric, although typically some species remain unobserved. Therefore, estimates of species richness and related quantities should account for imperfect detectability. Community dynamics can often be represented as superposition of species-specific phenologies (e. g., in taxa with well-defined flight [insects], activity [rodents], or vegetation periods [plants]). We develop a model for such predictably open communities wherein species richness is expressed as the sum over observed and unobserved species of estimated species-specific and site-specific occurrence indicators and where seasonal occurrence is modeled as a species-specific function of time. Our model is a multispecies extension of a multistate model with one unobservable state and represents a parsimonious way of dealing with a widespread form of 'temporary emigration.'' For illustration we use Swiss butterfly monitoring data collected under a robust design (RD); species were recorded on 13 transects during two secondary periods within <= 7 primary sampling periods. We compare estimates with those under a variation of the model applied to standard data, where secondary samples are pooled. The latter model yielded unrealistically high estimates of total community size of 274 species. In contrast, estimates were similar under models applied to RD data with constant (122) or seasonally varying (126) detectability for each species, but the former was more parsimonious and therefore used for inference. Per transect, 6 44 (mean 21.1) species were detected. Species richness estimates averaged 29.3; therefore only 71% (range 32-92%) of all species present were ever detected. In any primary period, 0.4-5.6 species present were overlooked. Detectability varied by species and averaged 0.88 per primary sampling period. Our modeling framework is extremely flexible; extensions such as covariates for the occurrence or detectability of individual species are easy. It should be useful for communities with a predictable form of temporary emigration where rigorous estimation of community metrics has proved challenging so far.

Ecology

Modeling the effects of environmental disturbance on wildlife communities: Avian responses to prescribed fire

Prescribed fire is a management tool used to reduce fuel loads on public lands in forested areas in the western United States. Identifying the impacts of prescribed fire on bird communities in ponderosa pine (Pinus ponderosa) forests is necessary for providing land management agencies with information regarding the effects of fuel reduction on sensitive, threatened, and migratory bird species. Recent developments in occupancy modeling have established a framework for quantifying the impacts of management practices on wildlife community dynamics. We describe a Bayesian hierarchical model of multi-species occupancy accounting for detection probability, and we demonstrate the model's usefulness for identifying effects of habitat disturbances on wildlife communities. Advantages to using the model include the ability to estimate the effects of environmental impacts on rare or elusive species, the intuitive nature of the modeling, the incorporation of detection probability, the estimation of parameter uncertainty, the flexibility of the model to suit a variety of experimental designs, and the composite estimate of the response that applies to the collection of observed species as opposed to merely a small subset of common species. Our modeling of the impacts of prescribed fire on avian communities in a ponderosa pine forest in Washington indicate that prescribed fire treatments result in increased occupancy rates for several bark-insectivore, cavity-nesting species including a management species of interest, Black-backed Woodpeckers (Picoides arcticus). Three aerial insectivore species, and the ground insectivore, American Robin (Turdus migratorius), also responded positively to prescribed fire, whereas three foliage insectivores and two seed specialists, Clark's Nutcracker (Nucifraga columbiana) and the Pine Siskin (Carduelis pinus), declined following treatments. Land management agencies interested in determining the effects of habitat manipulations on wildlife communities can use these methods to provide guidance for future management activities. ?? 2009 by the Ecological Society of America.

Ecological Applications

Inference about species richness and community structure using species-specific occupancy models in the National Swiss Breeding Bird Survey MUB

Species richness is the most widely used biodiversity measure. Virtually always, it cannot be observed but needs to be estimated because some species may be present but remain undetected. This fact is commonly ignored in ecology and management, although it will bias estimates of species richness and related parameters such as occupancy, turnover or extinction rates. We describe a species community modeling strategy based on species-specific models of occurrence, from which estimates of important summaries of community structure, e.g., species richness, occupancy, or measures of similarity among species or sites, are derived by aggregating indicators of occurrence for all species observed in the sample, and for the estimated complement of unobserved species. We use data augmentation for an efficient Bayesian approach to estimation and prediction under this model based on MCMC in WinBUGS. For illustration, we use the Swiss breeding bird survey (MHB) that conducts 2?3 territory-mapping surveys in a systematic sample of 267 1 km2 units on quadrat-specific routes averaging 5.1 km to obtain species-specific estimates of occupancy, and estimates of species richness of all diurnal species free of distorting effects of imperfect detectability. We introduce into our model species-specific covariates relevant to occupancy (elevation, forest cover, route length) and sampling (season, effort). From 1995 to 2004, 185 diurnal breeding bird species were known in Switzerland, and an additional 13 bred 1?3 times since 1900. 134 species were observed during MHB surveys in 254 quadrats surveyed in 2001, and our estimate of 169.9 (95% CI 151?195) therefore appeared sensible. The observed number of species ranged from 4 to 58 (mean 32.8), but with an estimated 0.7?11.2 (mean 2.6) further, unobserved species, the estimated proportion of detected species was 0.48?0.98 (mean 0.91). As is well known, species richness declined at higher elevation and fell above the timberline, and most species showed some preferred elevation. Route length had clear effects on occupancy, suggesting it is a proxy for the size of the effectively sampled area. Detection probability of most species showed clear seasonal patterns and increased with greater survey effort; these are important results for the planning of focused surveys. The main benefit of our model, and its implementation in WinBUGS for which we provide code, is its conceptual simplicity. Species richness is naturally expressed as the sum of occurrences of individual species. Information about species is combined across sites, which yields greater efficiency or may even enable estimation for sites with very few observed species in the first place. At the same time, species detections are clearly segregated into a true state process (occupancy) and an observation process (detection, given occupancy), and covariates can be readily introduced, which provides for efficient introduction of such additional information as well as sharp testing of such relationships.

Book chapter

Hierarchical models for estimating density from DNA mark-recapture studies

Genetic sampling is increasingly used as a tool by wildlife biologists and managers to estimate abundance and density of species. Typically, DNA is used to identify individuals captured in an array of traps ( e. g., baited hair snares) from which individual encounter histories are derived. Standard methods for estimating the size of a closed population can be applied to such data. However, due to the movement of individuals on and off the trapping array during sampling, the area over which individuals are exposed to trapping is unknown, and so obtaining unbiased estimates of density has proved difficult. We propose a hierarchical spatial capture-recapture model which contains explicit models for the spatial point process governing the distribution of individuals and their exposure to (via movement) and detection by traps. Detection probability is modeled as a function of each individual's distance to the trap. We applied this model to a black bear (Ursus americanus) study conducted in 2006 using a hair-snare trap array in the Adirondack region of New York, USA. We estimated the density of bears to be 0.159 bears/km2, which is lower than the estimated density (0.410 bears/km2) based on standard closed population techniques. A Bayesian analysis of the model is fully implemented in the software program WinBUGS.

Ecology

Bayesian inference in camera trapping studies for a class of spatial capture-recapture models

We develop a class of models for inference about abundance or density using spatial capture-recapture data from studies based on camera trapping and related methods. The model is a hierarchical model composed of two components: a point process model describing the distribution of individuals in space (or their home range centers) and a model describing the observation of individuals in traps. We suppose that trap- and individual-specific capture probabilities are a function of distance between individual home range centers and trap locations. We show that the models can be regarded as generalized linear mixed models, where the individual home range centers are random effects. We adopt a Bayesian framework for inference under these models using a formulation based on data augmentation. We apply the models to camera trapping data on tigers from the Nagarahole Reserve, India, collected over 48 nights in 2006. For this study, 120 camera locations were used, but cameras were only operational at 30 locations during any given sample occasion. Movement of traps is common in many camera-trapping studies and represents an important feature of the observation model that we address explicitly in our application.

Ecology

Trends in anuran occupancy from northeastern states of the North American Monitoring Program

We present the first multi-year occupancy trends from North American Amphibian Monitoring Program (NAAMP) data in 10 northeastern states using seven years of data (2001-2007). NAAMP uses a calling survey technique where observers listen for anuran vocalizations along assigned random roadside routes. We were able to assess occupancy trends in 10 northeastern states for 16 species and one species complex, for 94 species/state combinations. We found no significant trends for 64 species/state combinations. For the remaining 30 species/state combinations with significant trends, these split between declining and increasing trends. On a species-by-species basis, two species had declining trends, with significant trends in six states for Pseudacris crucifer and four states for Bufo americanus . The trends of Rana catesbeiana significantly increased in four states, but had no trend in the remaining states.

Herpetological Conservation and Biology

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Book

Modeling individual effects in the Cormack-Jolly-Seber Model: A state-space formulation

In population and evolutionary biology, there exists considerable interest in individual heterogeneity in parameters of demographic models for open populations. However, flexible and practical solutions to the development of such models have proven to be elusive. In this article, I provide a state-space formulation of open population capture-recapture models with individual effects. The state-space formulation provides a generic and flexible framework for modeling and inference in models with individual effects, and it yields a practical means of estimation in these complex problems via contemporary methods of Markov chain Monte Carlo. A straightforward implementation can be achieved in the software package WinBUGS. I provide an analysis of a simple model with constant parameter detection and survival probability parameters. A second example is based on data from a 7-year study of European dippers, in which a model with year and individual effects is fitted.

Biometrics

Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys

1. Species richness is the most widely used biodiversity metric, but cannot be observed directly as, typically, some species are overlooked. Imperfect detectability must therefore be accounted for to obtain unbiased species-richness estimates. When richness is assessed at multiple sites, two approaches can be used to estimate species richness: either estimating for each site separately, or pooling all samples. The first approach produces imprecise estimates, while the second loses site-specific information. 2. In contrast, a hierarchical Bayes (HB) multispecies site-occupancy model benefits from the combination of information across sites without losing site-specific information and also yields occupancy estimates for each species. The heart of the model is an estimate of the incompletely observed presence-absence matrix, a centrepiece of biogeography and monitoring studies. We illustrate the model using Swiss breeding bird survey data, and compare its estimates with the widely used jackknife species-richness estimator and raw species counts. 3. Two independent observers each conducted three surveys in 26 1-km(2) quadrats, and detected 27-56 (total 103) species. The average estimated proportion of species detected after three surveys was 0.87 under the HB model. Jackknife estimates were less precise (less repeatable between observers) than raw counts, but HB estimates were as repeatable as raw counts. The combination of information in the HB model thus resulted in species-richness estimates presumably at least as unbiased as previous approaches that correct for detectability, but without costs in precision relative to uncorrected, biased species counts. 4. Total species richness in the entire region sampled was estimated at 113.1 (CI 106-123); species detectability ranged from 0.08 to 0.99, illustrating very heterogeneous species detectability; and species occupancy was 0.06-0.96. Even after six surveys, absolute bias in observed occupancy was estimated at up to 0.40. 5. Synthesis and applications. The HB model for species-richness estimation combines information across sites and enjoys more precise, and presumably less biased, estimates than previous approaches. It also yields estimates of several measures of community size and composition. Covariates for occupancy and detectability can be included. We believe it has considerable potential for monitoring programmes as well as in biogeography and community ecology.

Journal of Applied Ecology

Hierarchical modeling of cluster size in wildlife surveys

Clusters or groups of individuals are the fundamental unit of observation in many wildlife sampling problems, including aerial surveys of waterfowl, marine mammals, and ungulates. Explicit accounting of cluster size in models for estimating abundance is necessary because detection of individuals within clusters is not independent and detectability of clusters is likely to increase with cluster size. This induces a cluster size bias in which the average cluster size in the sample is larger than in the population at large. Thus, failure to account for the relationship between delectability and cluster size will tend to yield a positive bias in estimates of abundance or density. I describe a hierarchical modeling framework for accounting for cluster-size bias in animal sampling. The hierarchical model consists of models for the observation process conditional on the cluster size distribution and the cluster size distribution conditional on the total number of clusters. Optionally, a spatial model can be specified that describes variation in the total number of clusters per sample unit. Parameter estimation, model selection, and criticism may be carried out using conventional likelihood-based methods. An extension of the model is described for the situation where measurable covariates at the level of the sample unit are available. Several candidate models within the proposed class are evaluated for aerial survey data on mallard ducks (Anas platyrhynchos).

Journal of Agricultural, Biological, and Environme

Importance of sampling design and analysis in animal population studies: a comment on Sergio et al

1. The use of predators as indicators and umbrellas in conservation has been criticized. In the Trentino region, Sergio et al. (2006; hereafter SEA) counted almost twice as many bird species in quadrats located in raptor territories than in controls. However, SEA detected astonishingly few species. We used contemporary Swiss Breeding Bird Survey data from an adjacent region and a novel statistical model that corrects for overlooked species to estimate the expected number of bird species per quadrat in that region. 2. There are two anomalies in SEA which render their results ambiguous. First, SEA detected on average only 6.8 species, whereas a value of 32 might be expected. Hence, they probably overlooked almost 80% of all species. Secondly, the precision of their mean species counts was greater in two-thirds of cases than in the unlikely case that all quadrats harboured exactly the same number of equally detectable species. This suggests that they detected consistently only a biased, unrepresentative subset of species. 3. Conceptually, expected species counts are the product of true species number and species detectability p. Plenty of factors may affect p, including date, hour, observer, previous knowledge of a site and mobbing behaviour of passerines in the presence of predators. Such differences in p between raptor and control quadrats could have easily created the observed effects. Without a method that corrects for such biases, or without quantitative evidence that species detectability was indeed similar between raptor and control quadrats, the meaning of SEA's counts is hard to evaluate. Therefore, the evidence presented by SEA in favour of raptors as indicator species for enhanced levels of biodiversity remains inconclusive. 4. Synthesis and application. Ecologists should pay greater attention to sampling design and analysis in animal population estimation. Species richness estimation means sampling a community. Samples should be representative for the community studied and the sampling fraction among communities compared should be the same on average, otherwise formal estimation approaches must be applied to avoid misleading inference.

Journal of Applied Ecology

A hierarchical model for spatial capture-recapture data

Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.

Ecology

A double-observer method to estimate detection rate during aerial waterfowl surveys

We evaluated double-observer methods for aerial surveys as a means to adjust counts of waterfowl for incomplete detection. We conducted our study in eastern Canada and the northeast United States utilizing 3 aerial-survey crews flying 3 different types of fixed-wing aircraft. We reconciled counts of front- and rear-seat observers immediately following an observation by the rear-seat observer (i.e., on-the-fly reconciliation). We evaluated 6 a priori models containing a combination of several factors thought to influence detection probability including observer, seat position, aircraft type, and group size. We analyzed data for American black ducks (Anas rubripes) and mallards (A. platyrhynchos), which are among the most abundant duck species in this region. The best-supported model for both black ducks and mallards included observer effects. Sample sizes of black ducks were sufficient to estimate observer-specific detection rates for each crew. Estimated detection rates for black ducks were 0.62 (SE = 0.10), 0.63 (SE = 0.06), and 0.74 (SE = 0.07) for pilot-observers, 0.61 (SE = 0.08), 0.62 (SE = 0.06), and 0.81 (SE = 0.07) for other front-seat observers, and 0.43 (SE = 0.05), 0.58 (SE = 0.06), and 0.73 (SE = 0.04) for rear-seat observers. For mallards, sample sizes were adequate to generate stable maximum-likelihood estimates of observer-specific detection rates for only one aerial crew. Estimated observer-specific detection rates for that crew were 0.84 (SE = 0.04) for the pilot-observer, 0.74 (SE = 0.05) for the other front-seat observer, and 0.47 (SE = 0.03) for the rear-seat observer. Estimated observer detection rates were confounded by the position of the seat occupied by an observer, because observers did not switch seats, and by land-cover because vegetation and landform varied among crew areas. Double-observer methods with on-the-fly reconciliation, although not without challenges, offer one viable option to account for detection bias in aerial waterfowl surveys where birds are distributed at low density in remote areas that are inaccessible by ground crews. Double-observer methods, however, estimate only detection rate of animals that are potentially observable given the survey method applied. Auxiliary data and methods must be considered to estimate overall detection rate.

Journal of Wildlife Management

Population influences on tornado reports in the United States

The number of tornadoes reported in the United States is believed to be less than the actual incidence of tornadoes, especially prior to the 1990s, because tornadoes may be undetectable by human witnesses in sparsely populated areas and areas in which obstructions limit the line of sight. A hierarchical Bayesian model is used to simultaneously correct for population-based sampling bias and estimate tornado density using historical tornado report data. The expected result is that F2-F5 compared with F0-F1 tornado reports would vary less with population density. The results agree with this hypothesis for the following population centers: Atlanta, Georgia; Champaign, Illinois; and Des Moines, Iowa. However, the results indicated just the opposite in Oklahoma. It is hypothesized that the result is explained by the misclassification of tornadoes that were worthy of F2-F5 rating but were classified as F0-F1 tornadoes, thereby artificially decreasing the number of F2-F5 and increasing the number of F0-F1 reports in rural Oklahoma.

Weather and Forecasting

Hierarchical spatiotemporal matrix models for characterizing invasions

The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing. ?? 2006, The International Biometric Society.

Biometrics