scholarly journals Bayesian analysis to correct false-negative errors in capture–recapture photo-ID abundance estimates

2009 ◽  
Vol 23 (1) ◽  
pp. 36-48 ◽  
Author(s):  
Cibele Q. da-Silva
Keyword(s):  
Bayesian Analysis ◽  
False Negative ◽  
Abundance Estimates ◽  
Capture Recapture

Errors in identification using natural markings: rates, sources, and effects on capture–recapture estimates of abundance

2001 ◽  
Vol 58 (9) ◽  
pp. 1861-1870 ◽  
Author(s):  
Peter T Stevick ◽  
Per J Palsbøll ◽  
Tim D Smith ◽  
Mark V Bravington ◽  
Philip S Hammond
Keyword(s):  
Error Rate ◽  
Large Scale ◽  
False Negative ◽  
Parametric Bootstrap ◽  
Humpback Whales ◽  
The North ◽  
Abundance Estimates ◽  
Capture Recapture ◽  
Quality Rating ◽  
Estimation Of Variance

The results of a double-marking experiment using natural markings and microsatellite genetic markers to identify humpback whales (Megaptera novaeangliae) confirm that natural markings are a reliable means of identifying individuals on a large scale. Of 1410 instances of double tagging, there were 414 resightings. No false positive and 14 false negative errors were identified. The rate of error increased with decreasing photographic quality; no errors were observed among photographs of the highest quality rating, whereas an error rate of 0.125 was identified in sightings for which only part of the area used for identification was visible. There was also a weaker relationship between error rate and the distinctiveness of markings, which may result from non-independence in coding for image quality and distinctiveness. A correction is developed for the Petersen two-sample abundance estimator to account for false negative errors in identification, and a parametric bootstrap procedure for estimation of variance is also developed. In application to abundance estimates from the North Atlantic, the correction reduces the bias in estimates made using poorer quality photographs to a negligible level while maintaining comparable precision.

Multiple challenges confront a high-effort inland recreational fishery in decline

2018 ◽  
Vol 75 (9) ◽  
pp. 1357-1368 ◽  
Author(s):  
Christopher L. Cahill ◽  
Stephanie Mogensen ◽  
Kyle L. Wilson ◽  
Ariane Cantin ◽  
R. Nilo Sinnatamby ◽  
...  
Keyword(s):  
Multiple Stressors ◽  
Fishing Effort ◽  
Population Declines ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Abundance Estimates ◽  
Sampling Locations ◽  
Management Perspective ◽  
Capture Recapture ◽  
Multiple Challenges ◽  
High Effort

Catch-and-release regulations designed to protect fisheries may fail to halt population declines, particularly in situations where fishing effort is high and when multiple stressors threaten a population. We demonstrate this claim using Alberta’s Bow River, which supports a high-effort rainbow trout (Oncorhynchus mykiss) fishery where anglers voluntarily release >99% of their catch. We examined the population trend of adult trout, which were tagged and recaptured using electrofishing surveys conducted intermittently during 2003–2013. We constructed Bayesian multisession capture–recapture models in Stan to obtain abundance estimates for trout and regressed trend during two periods to account for variation in sampling locations. General patterns from all models indicated the population declined throughout the study. Potential stressors to this system that may have contributed to the decline include whirling disease (Myxobolus cerebralis), which was detected for the first time in 2016, notable floods, and release mortality. Because disease and floods are largely uncontrollable from a management perspective, we suggest that stringent tactics such as angler effort restrictions may be necessary to maintain similar fisheries.

scholarly journals On the Estimation of Dispersal and Movement of Birds

The Condor ◽  
2004 ◽  
Vol 106 (4) ◽  
pp. 720-731 ◽  
Author(s):  
William L. Kendall ◽  
James D. Nichols
Keyword(s):  
Robust Design ◽  
Nonlinear Dynamic ◽  
Detection Probability ◽  
Cross Correlation ◽  
Statistical Methodology ◽  
Open Population ◽  
Abundance Estimates ◽  
Capture Recapture ◽  
Over Time

Abstract The estimation of dispersal and movement is important to evolutionary and population ecologists, as well as to wildlife managers. We review statistical methodology available to estimate movement probabilities. We begin with cases where individual birds can be marked and their movements estimated with the use of multisite capture-recapture methods. Movements can be monitored either directly, using telemetry, or by accounting for detection probability when conventional marks are used. When one or more sites are unobservable, telemetry, band recoveries, incidental observations, a closed- or open-population robust design, or partial determinism in movements can be used to estimate movement. When individuals cannot be marked, presence-absence data can be used to model changes in occupancy over time, providing indirect inferences about movement. Where abundance estimates over time are available for multiple sites, potential coupling of their dynamics can be investigated using linear cross-correlation or nonlinear dynamic tools. Sobre la Estimación de la Dispersión y el Movimiento de las Aves Resumen. La estimación de la dispersión y el movimiento es importante para los ecó logos evolutivos y de poblaciones, así como también para los encargados del manejo de vida silvestre. Revisamos la metodología estadística disponible para estimar probabilidades de movimiento. Empezamos con casos donde aves individuales pueden ser marcadas y sus movimientos estimados con el uso de métodos de captura-repactura para múltiples sitios. Los movimientos pueden ser monitoreados ya sea directamente, usando telemetría o teniendo en cuenta las probabilidades de detección cuando se usan marcas convencionales. Cuando uno o más sitios no pueden ser observados, se puede estimar el movimiento usando telemetría, recuperación de anillos, observaciones circunstanciales, un diseño poblacional robusto cerrado o abierto, o determinismo parcial de los movimientos. Cuando los individuos no pueden ser marcados, se pueden usar datos de presencia-ausencia para modelar los cambios en el tiempo de la ocupación, brindando inferencias indirectas sobre los movimientos. Cuando las estimaciones de abundancia a lo largo del tiempo están disponibles para varios sitios, se puede investigar la interrelación potencial de sus dinámicas usando correlaciones cruzadas lineales o herramientas para dinámica no lineal.

scholarly journals Abundance, survival and temporary emigration of bottlenose dolphins (Tursiops sp.) off Useless Loop in the western gulf of Shark Bay, Western Australia

2012 ◽  
Vol 63 (11) ◽  
pp. 1059 ◽  
Author(s):  
Krista Nicholson ◽  
Lars Bejder ◽  
Simon J. Allen ◽  
Michael Krützen ◽  
Kenneth H. Pollock
Keyword(s):  
Western Australia ◽  
Bottlenose Dolphins ◽  
Early Spring ◽  
Anthropogenic Activity ◽  
Apparent Survival ◽  
Photo Identification ◽  
Temporary Emigration ◽  
Shark Bay ◽  
Abundance Estimates ◽  
Capture Recapture

Capture–recapture models were used to provide estimates of abundance, apparent survival and temporary emigration of Indo-Pacific bottlenose dolphins (Tursiops sp.) in a 226-km2 study area off Useless Loop in the western gulf of Shark Bay, Western Australia. Photo-identification data were collected during boat-based surveys in Austral autumn to early spring (April–September) from 2007 to 2011. Abundance estimates varied from 115 (s.e. 5.2, 95% CI 105–126) individuals in 2008 to 208 (s.e. 17.3, 95% CI 177–245) individuals in 2010. The variability in abundance estimates is likely to be a reflection of how individuals used the study area, rather than fluctuations in true population size. The best fitting capture–recapture model suggested a random temporary emigration pattern and, when coupled with relatively high temporary emigration rates (0.33 (s.e. 0.07) – 0.66 (s.e. 0.05)) indicated that the study area did not cover the entire ranges of the photo-identified dolphins. Apparent survival rate is a product of true survival and permanent emigration and was estimated annually at 0.95 (s.e. 0.02). Since permanent emigration from the study area is unlikely, true survival was estimated to be close to 0.95. This study provides a robust baseline for future comparisons of dolphin demographics, which may be of importance should climate change or increasing anthropogenic activity affect this population.

scholarly journals First estimation of Eurasian lynx (Lynx lynx) abundance and density using digital cameras and capture–recapture techniques in a German national park

2012 ◽  
Vol 35 (2) ◽  
pp. 197-207 ◽  
Author(s):  
K. Weingarth ◽  
◽  
C. Heibl ◽  
F. Knauer ◽  
F. Zimmermann ◽  
...  
Keyword(s):  
National Park ◽  
Large Scale ◽  
Lynx Lynx ◽  
Digital Cameras ◽  
The European Union ◽  
Eurasian Lynx ◽  
Habitat Directive ◽  
Abundance Estimates ◽  
Capture Recapture

Eurasian lynx are individually identifiable by their unique coat markings, making them ideal candidates for capture–recapture (CMR) surveys. We evaluated the use of digital photography to estimate Eurasian lynx population abundance and density within the Bavarian Forest National Park. From November 2008 to January 2009 we placed 24 camera trap sites, each with two cameras facing each other on well–used walking tracks). The units were placed based on a systematic grid of 2.7 km. We captured five independent and three juvenile lynx and calculated abundance estimates using Program Mark. We also compared density estimates based on the MMDM method (Mean Maximum Distance Moved) from telemetry data (½MMDMGPS) and from camera trapping data (½MMDMCAM). We estimated that in an effectively sampled area of 664 km2 the Eurasian lynx density was 0.9 individuals/100 km2 with ½MMDMCAM. The Eurasian lynx density calculated with ½MMDMGPS was 0.4 individuals/100 km2 in an effectively sampled area of 1,381 km2. Our results suggest that long–term photographic CMR sampling on a large scale may be a useful tool to monitor population trends of Eurasian lynx in accordance with the Fauna–Flora–Habitat Directive of the European Union.

scholarly journals Abundance of East coast Australian humpback whales (Megaptera novaeangliae) in 2005 estimated using multi-point sampling and capture-recapture analysis

2020 ◽  
pp. 253-259
Author(s):  
David A. Paton ◽  
Lyndon Brooks ◽  
Daniel Burns ◽  
Trish Franklin ◽  
Wally Franklin ◽  
...  
Keyword(s):  
East Coast ◽  
Megaptera Novaeangliae ◽  
Humpback Whales ◽  
Migration Route ◽  
Closed Population ◽  
Breeding Stock ◽  
Abundance Estimate ◽  
Abundance Estimates ◽  
Capture Recapture ◽  
Near Extinction

The humpback whales (Megaptera novaeangliae) that migrate along the east coast of Australia were hunted to near extinction during the lastcentury. This remnant population is part of Breeding Stock E. Previous abundance estimates for the east Australian portion of Breeding Stock Ehave been based mainly on land-based counts. Here we present a capture-recapture abundance estimate for this population using photo-identificationdata. These data were collected at three locations on the migration route (Byron Bay – northern migration, Hervey Bay and Ballina – southernmigration) in order to estimate the population of humpback whales that migrated along the east coast of Australia in 2005. The capture-recapturedata were analysed using a variety of closed population models with a model-averaged estimate of 7,041 (95% CI 4,075–10,008) whales.

Application of Capture-Recapture Methods for Disease Monitoring: Potential Effects of Imperfect Record Linkage

1994 ◽  
Vol 33 (05) ◽  
pp. 502-506 ◽  
Author(s):  
H. Brenner
Keyword(s):  
Record Linkage ◽  
False Positive ◽  
Quantitative Assessment ◽  
False Negative ◽  
Monitoring Systems ◽  
Disease Monitoring ◽  
Correction Procedure ◽  
Case Ascertainment ◽  
Capture Recapture

Abstract:Capture-recapture methods are increasingly employed to correct for underascertainment of cases in disease monitoring. Routine systems of disease monitoring, such as morbidity registries, are often prone to specific threats of validity, such as in imperfect diagnoses or imperfect record linkage. A quantitative assessment is given of the performance of the two-source capture-recapture method for disease monitoring in the presence of imperfect record linkage. The capture-recapture approach can eliminate underestimation of the number of eligible cases, which is typical for most disease monitoring systems, under certain conditions, including independence of sources of case ascertainment and perfect record linkage. Correction for underestimation remains less than perfect, however, in the case of false-positive matches, whereas application of capture-recapture methods leads to overestimation of case numbers in the presence of false-negative matches. A simple correction procedure to overcome potential overestimation by false-negative matches is outlined.

scholarly journals Complete tag loss in capture–recapture studies affects abundance estimates: An elephant seal case study

2020 ◽  
Vol 10 (5) ◽  
pp. 2377-2384
Author(s):  
Emily Malcolm‐White ◽  
Clive R. McMahon ◽  
Laura L. E. Cowen
Keyword(s):  
Elephant Seal ◽  
Tag Loss ◽  
Abundance Estimates ◽  
Capture Recapture

scholarly journals A spatially explicit approach for estimating space use and density of common genets

2014 ◽  
Vol 37 (1) ◽  
pp. 23-33
Author(s):  
P. Sarmento ◽  
◽  
J. Cruz ◽  
C. Eira ◽  
C. Fonseca ◽  
...  
Keyword(s):  
Spatial Model ◽  
Environmental Variables ◽  
Camera Trap ◽  
Grid Size ◽  
Future Research ◽  
Spatially Explicit ◽  
Density Estimates ◽  
Closed Population ◽  
Abundance Estimates ◽  
Capture Recapture

Many species that occur at low densities are not accurately estimated using capture–recapture methods as such techniques assume that populations are well–defined in space. To solve this bias, spatially explicit capture–recapture (SECR) models have recently been developed. These models incorporate movement and can identify areas where it is more likely for individuals to concentrate their activity. In this study, we used data from camera–trap surveys of common genets (Genetta genetta) in Serra da Malcata (Portugal), designed to compare abundance estimates produced by SECR models with traditional closed–capture models. Using the SECR models, we observed spatial heterogeneity in genet distribution and density estimates were approximately two times lower than those obtained from the closed population models. The non–spatial model estimates were constrained to sampling grid size and likely underestimated movements, thereby overestimating density. Future research should consider the incorporation of cost–weighed models that can include explicit hypothesis on how environmental variables influence the distance metric.

scholarly journals Visual Head Counts: A Promising Method for Efficient Monitoring of Diamondback Terrapins

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 101 ◽  
Author(s):  
Patricia Levasseur ◽  
Sean Sterrett ◽  
Chris Sutherland
Keyword(s):  
Count Data ◽  
Hierarchical Modeling ◽  
Spatial Scales ◽  
Diamondback Terrapin ◽  
Imperfect Detection ◽  
Modeling Framework ◽  
Abundance Estimates ◽  
Invasive Method ◽  
Capture Recapture ◽  
Diamondback Terrapins

Determining the population status of the diamondback terrapin (Malaclemys terrapin spp.) is challenging due to their ecology and limitations associated with traditional sampling methods. Visual counting of emergent heads offers a promising, efficient, and non-invasive method for generating abundance estimates of terrapin populations across broader spatial scales than has been achieved using capture–recapture, and can be used to quantify determinants of spatial variation in abundance. We conducted repeated visual head count surveys along the shoreline of Wellfleet Bay in Wellfleet, Massachusetts, and analyzed the count data using a hierarchical modeling framework designed specifically for repeated count data: the N-mixture model. This approach allows for simultaneous modeling of imperfect detection to generate estimates of true terrapin abundance. Detection probability was lowest when temperatures were coldest and when wind speed was highest. Local abundance was on average higher in sheltered sites compared to exposed sites and declined over the course of the sampling season. We demonstrate the utility of pairing visual head counts and N-mixture models as an efficient method for estimating terrapin abundance and show how the approach can be used to identifying environmental factors that influence detectability and distribution.

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