Integrating imputation and standardization of catch rate data in the calculation of relative abundance indices

2011 ◽  
Vol 109 (1) ◽  
pp. 157-167 ◽  
Author(s):  
Thomas R. Carruthers ◽  
Robert N.M. Ahrens ◽  
Murdoch K. McAllister ◽  
Carl J. Walters
Keyword(s):  
Relative Abundance ◽  
Catch Rate ◽  
Rate Data ◽  
Abundance Indices

Folly and fantasy in the analysis of spatial catch rate data

2003 ◽  
Vol 60 (12) ◽  
pp. 1433-1436 ◽  
Author(s):  
Carl Walters
Keyword(s):  
Catch Rate ◽  
Population Trends ◽  
Rate Data ◽  
Fishing Activity ◽  
Time Period ◽  
Abundance Indices ◽  
Catch Rates ◽  
Catch Per Effort

Spatial catch per effort data can provide useful indices of population trends provided that they are averaged so as to correct for effects of changes in the distribution of fishing activity. Simple, nonspatial ratio estimates should not be used in such analyses. The averaging for any time period must necessarily make some assumptions about what catch rates would have been in spatial strata that had not yet, or were no longer, being fished. Ignoring the unfished strata (averaging only over the areas that were fished) amounts to assuming that they behaved the same as the fished strata and can lead to severe hyperdepletion in abundance indices for fisheries that developed progressively over large regions.

scholarly journals Integrating spatial synchrony/asynchrony of population distribution into stock assessment models: a spatial hierarchical Bayesian statistical catch-at-age approach

2016 ◽  
Vol 73 (7) ◽  
pp. 1725-1738 ◽  
Author(s):  
Yan Jiao ◽  
Rob O'Reilly ◽  
Eric Smith ◽  
Don Orth ◽  
Keyword(s):  
Relative Abundance ◽  
Bayesian Model ◽  
Population Distribution ◽  
Stock Assessment ◽  
Spatial Models ◽  
Reference Points ◽  
Hierarchical Bayesian ◽  
Hierarchical Bayesian Model ◽  
Spatial Synchrony ◽  
Abundance Indices

Abstract In many marine fisheries assessments, population abundance indices from surveys collected by different states and agencies do not always agree with each other. This phenomenon is often due to the spatial synchrony/asynchrony. Those indices that are asynchronous may result in discrepancies in the assessment of temporal trends. In addition, commonly employed stock assessment models, such as the statistical catch-at-age (SCA) models, do not account for spatial synchrony/asynchrony associated with spatial autocorrelation, dispersal, and environmental noise. This limits the value of statistical inference on key parameters associated with population dynamics and management reference points. To address this problem, a set of geospatial analyses of relative abundance indices is proposed to model the indices from different surveys using spatial hierarchical Bayesian models. This approach allows better integration of different surveys with spatial synchrony and asynchrony. We used Atlantic weakfish (Cynoscion regalis) as an example for which there are state-wide surveys and expansive coastal surveys. We further compared the performance of the proposed spatially structured hierarchical Bayesian SCA models with a commonly used Bayesian SCA model that assumes relative abundance indices are spatially independent. Three spatial models developed to mimic different potential spatial patterns were compared. The random effect spatially structured hierarchical Bayesian model was found to be better than the commonly used SCA model and the other two spatial models. A simulation study was conducted to evaluate the uncertainty resulting from model selection and the robustness of the recommended model. The spatially structured hierarchical Bayesian model was shown to be able to integrate different survey indices with/without spatial synchrony. It is suggested as a useful tool when there are surveys with different spatial characteristics that need to be combined in a fisheries stock assessment.

Comparison of odontocete populations of the Marquesas and Society Islands (French Polynesia)

2008 ◽  
Vol 89 (5) ◽  
pp. 931-941 ◽  
Author(s):  
Alexandre Gannier
Keyword(s):  
Relative Abundance ◽  
Bottlenose Dolphin ◽  
Bottlenose Dolphins ◽  
Sperm Whale ◽  
French Polynesia ◽  
Society Islands ◽  
Spotted Dolphin ◽  
Abundance Indices ◽  
Beaked Whales ◽  
Using Data

Small boat surveys were organized to study cetaceans of the Marquesas (9°S and 140°W) and the Society Islands (17°S and 150°W) in French Polynesia. Prospecting took place from 12–15 m sailboats, between 1996 and 2001 with systematic visual searching. Boats moved according to sea conditions, at a mean speed of 10 km/h. Effective effort of 4856 km in the Marquesas and 10,127 km in the Societies were logged. Relative abundance indices were processed for odontocetes using data obtained with Beaufort 4 or less. In the Marquesas, 153 on-effort sightings were obtained on 10 delphinids species including the spotted dolphin, spinner dolphin, bottlenose dolphin, melon-headed whale and rough-toothed dolphin. In the Societies, 153 sightings of 12 odontocetes included delphinids (spinner, rough-toothed and bottlenose dolphins, short-finned pilot and melon-headed whales, Fraser's dolphin, Risso's dolphin and pygmy killer whale) and two species of beaked whales, the sperm whale and dwarf sperm whale. Relative abundance indices were higher in the Marquesas than in the Societies both inshore (0.93 ind/km2 against 0.36 ind/km2) and offshore (0.28 ind/km2 against 0.14 ind/km2). Differences in remote-sensed primary production were equally important, the Marquesas waters featuring an annual average of 409 mgC.m−2 · day−1 and the Societies of only 171 mgC · m−2 · day−1. The presence of a narrow shelf around the Marquesas also accounted for differences in odontocete populations, in particular the delphinids.

scholarly journals Using catch rate data for simple cost-effective quota setting in the Australian spanner crab (Ranina ranina) fishery

2010 ◽  
Vol 67 (8) ◽  
pp. 1538-1552 ◽  
Author(s):  
Michael F. O'Neill ◽  
Alexander B. Campbell ◽  
Ian W. Brown ◽  
Ron Johnstone
Keyword(s):  
Decision Rules ◽  
Cost Effective ◽  
Catch Rate ◽  
Management Decision ◽  
Rate Data ◽  
Total Allowable Catch ◽  
Management Procedure ◽  
Annual Total ◽  
New Methodologies ◽  
Catch Rates

Abstract O'Neill, M. F., Campbell, A. B., Brown, I. W., and Johnstone, R. 2010. Using catch rate data for simple cost-effective quota setting in the Australian spanner crab (Ranina ranina) fishery. – ICES Journal of Marine Science, 67: 1538–1552. For many fisheries, there is a need to develop appropriate indicators, methodologies, and rules for sustainably harvesting marine resources. Complexities of scientific and financial factors often prevent addressing these, but new methodologies offer significant improvements on current and historical approaches. The Australian spanner crab fishery is used to demonstrate this. Between 1999 and 2006, an empirical management procedure using linear regression of fishery catch rates was used to set the annual total allowable catch (quota). A 6-year increasing trend in catch rates revealed shortcomings in the methodology, with a 68% increase in quota calculated for the 2007 fishing year. This large quota increase was prevented by management decision rules. A revised empirical management procedure was developed subsequently, and it achieved a better balance between responsiveness and stability. Simulations identified precautionary harvest and catch rate baselines to set quotas that ensured sustainable crab biomass and favourable performance for management and industry. The management procedure was simple to follow, cost-effective, robust to strong trends and changes in catch rates, and adaptable for use in many fisheries. Application of such “tried-and-tested” empirical systems will allow improved management of both data-limited and data-rich fisheries.

Evaluation of three relative abundance indices for assessing dingo populations

1996 ◽  
Vol 23 (2) ◽  
pp. 197 ◽  
Author(s):  
L Allen ◽  
R Engeman ◽  
H Krupa
Keyword(s):  
Relative Abundance ◽  
Canis Lupus ◽  
Activity Index ◽  
Correlation Coefficients ◽  
Target Species ◽  
Wild Canids ◽  
Population Reduction ◽  
Abundance Indices ◽  
High Level ◽  
Level Of Agreement

Three methods of assessing relative abundance of wild canids were evaluated on a population of dingoes, Canis lupus dingo (Corbett), on a cattle station in south-westem Queensland. The tested indices relied on measurements of activity based on spoor. Two of the techniques attracted the target species to tracking stations through the use of a novel (fatty acid scent) or food-based (buried meat) attractant. The third index (activity) measured the number of dingo tracks crossing tracking stations placed at 1-km intervals along a road transect. All three indices had a high level of agreement for detecting differences in relative abundance, with correlation coefficients exceeding 0.85. When the stations were analysed in 1-km segments, the activity index proved the most sensitive, producing proportionally more positive responses than either of the other two indices irrespective of whether the tracking stations were assessed at 1-, 2-, 3- or 4-day intervals. Inconsistencies between indices existed, with the derived abundance indices not showing the anticipated reduction following population reduction. The effect of season and the interaction between dingo activity and index methodology are discussed.

Evaluation of spatiotemporal imputations for fishing catch rate standardization

2017 ◽  
Vol 74 (9) ◽  
pp. 1348-1361
Author(s):  
Ross J. Marriott ◽  
Berwin A. Turlach ◽  
Kevin Murray ◽  
David V. Fairclough
Keyword(s):  
High Growth ◽  
Catch Rate ◽  
Commercial Fishing ◽  
Data Sets ◽  
Rate Data ◽  
Fishing Activity ◽  
Fish Stocks ◽  
Base Method ◽  
Catch Rates ◽  
Over Time

As commercial fishing activity shifts to target different grounds over time, spatial gaps can be created in catch rate data, leading to biases in derived indices of fish abundance. Imputation has been shown to reduce such biases. In this study, the relative performance of several imputation methods was assessed using simulated catch rate data sets. Simulations were carried out for three fish stocks targeted by a commercial hook-and-line fishery off the southwestern coast of Australia: snapper (Chrysophrys auratus), West Australian dhufish (Glaucosoma hebraicum), and baldchin groper (Choerodon rubescens). For high-growth scenarios, the mean squared errors (MSEs) of geometric and linear imputations were lower, indicating higher accuracy and precision than that for base method (constant value) imputations. For low-growth scenarios, the lowest MSEs were achieved for base method imputations. However, for the final standardized and imputed abundance indices, the base method index consistently demonstrated the largest biases. Our results demonstrate the importance of selecting an appropriate imputation method when standardizing catch rates from a commercial fishery that has changed its spatial pattern of fishing over time.

Accounting for marine reserves using spatial stock assessments

2015 ◽  
Vol 72 (2) ◽  
pp. 262-280 ◽  
Author(s):  
Carey R. McGilliard ◽  
André E. Punt ◽  
Richard D. Methot ◽  
Ray Hilborn
Keyword(s):  
Spatial Heterogeneity ◽  
Stock Assessment ◽  
Marine Reserves ◽  
Movement Patterns ◽  
Catch Rate ◽  
Fish Stock ◽  
Rate Data ◽  
Stock Assessments ◽  
Age Structured ◽  
Movement Parameters

Some fish stock assessments are conducted in regions that contain no-take marine reserves (NTMRs). NTMRs are expected to lead to spatial heterogeneity in fish biomass by allowing a buildup of biomass inside their borders while fishing pressure occurs outside. Stock assessments do not typically account for spatial heterogeneity caused by NTMRs, which may lead to biased estimates of biomass. Simulation modeling is used to analyze the ability of several stock assessment configurations to estimate current biomass after the implementation of a single, large NTMR. Age-structured spatial operating models with three patterns of ontogenetic movement are used to represent the “true” population dynamics. Results show that assessing populations as a single stock with use of fishery catch-rate data and without accounting for the NTMR results in severe underestimation of biomass for two of the movement patterns. Omitting fishery catch-rate data or allowing time-varying dome-shaped selectivity after NTMR implementation leads to improved estimates of current biomass, but severe bias in estimated trends in biomass over time. Performing separate assessments for fished areas and NTMRs leads to improved estimation performance in the absence of movement among assessment areas, but can severely overestimate biomass otherwise. Performing a spatial assessment with estimation of movement parameters among areas was found to be the best way to assess a species, even when movement patterns were unknown. However, future work should explore the performance of spatial assessments when catchability varies among areas.

scholarly journals Evaluation of Potential Overwinter Mortality of Age-0 Walleye and Appropriate Age-1 Sampling Gear

2018 ◽  
Vol 9 (1) ◽  
pp. 65-74 ◽  
Author(s):  
Jeffrey D. Grote ◽  
Melissa R. Wuellner ◽  
Brian G. Blackwell ◽  
David O. Lucchesi
Keyword(s):  
South Dakota ◽  
Body Condition ◽  
Relative Abundance ◽  
Coefficient Of Variation ◽  
First Year ◽  
Selective Mortality ◽  
Frequency Distributions ◽  
Abundance Indices ◽  
Overwinter Mortality ◽  
First Year Of Life

Abstract Potential recruitment of age-0 Walleye Sander vitreus to adults is often indexed by the relative abundance of age-0 individuals during their first summer or fall. However, relationships between age-0 and adult Walleye abundance are often weak or nonsignificant in many waters. Overwinter mortality during the first year of life has been hypothesized as an important limitation to Walleye recruitment in lakes, but limited evidence of such mortality exists, likely due to difficulties in sampling age-1 Walleye during spring. The objectives of this study were to: 1) compare results from nighttime electrofishing to index relative abundance of age-1 Walleyes with relative abundance indices of minifyke nets in four eastern South Dakota lakes; 2) determine whether size-selective mortality was occurring in those four lakes; and 3) if size-selective mortality was occurring in these lakes, determine whether that mortality was attributed to body condition. We sampled four natural lakes in eastern South Dakota 2 wk after ice-off in 2013 and 2014. Precision of nighttime electrofishing (coefficient of variation = 216.6) was greater than that estimated for minifyke nets (coefficient of variation = 338.5) across both years. We detected no differences in length-frequency distributions of collected spring age-1 Walleye between the two gears. Age-0 fall relative abundance indices from electrofishing were significantly greater (P < 0.01) than spring age-1 nighttime electrofishing indices of relative abundance at three of the four study lakes, indicating that overwinter mortality may occur at a substantial rate during the first year of life for Walleye in these systems. Quantile–quantile regression plots showed evidence of size-selective mortality in three of four lakes sampled. However, body condition of age-0 Walleye appeared to have little to no influence on overwinter mortality. Instead, we suggest that smaller-sized walleye may be more vulnerable to overwinter predation. Collectively, these results provide evidence of previously hypothesized overwinter mortality within the first year for Walleye and indicate possibilities for indexing potential adult recruitment of Walleye just after this critical period.

scholarly journals The geometric mean of relative abundance indices: a biodiversity measure with a difference

Ecosphere ◽  
2011 ◽  
Vol 2 (9) ◽  
pp. art100 ◽  
Author(s):  
Stephen T. Buckland ◽  
Angelika C. Studeny ◽  
Anne E. Magurran ◽  
Janine B. Illian ◽  
Stuart E. Newson
Keyword(s):  
Relative Abundance ◽  
Geometric Mean ◽  
Abundance Indices
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