Spatiotemporal modelling for the annual egg production method of stock assessment using generalized additive models

1998 ◽  
Vol 55 (12) ◽  
pp. 2608-2621 ◽  
Author(s):  
N H Augustin ◽  
D L Borchers ◽  
E D Clarke ◽  
S T Buckland ◽  
M Walsh
Keyword(s):  
Environmental Variables ◽  
Egg Production ◽  
Survey Design ◽  
Stock Assessment ◽  
Generalized Additive Models ◽  
Production Method ◽  
Additive Models ◽  
Atlantic Mackerel ◽  
Egg Density ◽  
Survey Designs

Generalized additive models (GAMs) are used to model the spatiotemporal distribution of egg density as a function of locational and environmental variables. The main aim of using GAMs is to improve precision of egg abundance estimates needed for the annual egg production method. The application of GAMs requires a survey design with good coverage in space and time. If the only results available are from less optimal survey designs, they can be improved by using historical data for spawning boundaries. The method is applied to plankton egg survey data of Atlantic mackerel (Scomber scombrus) in 1995. The GAM-based method improves the precision of estimates substantially and is also useful in explaining complex space-time trends using environmental variables.

Improving the precision of the daily egg production method using generalized additive models

1997 ◽  
Vol 54 (12) ◽  
pp. 2727-2742 ◽  
Author(s):  
D L Borchers ◽  
S T Buckland ◽  
I G Priede ◽  
S Ahmadi
Keyword(s):  
Egg Production ◽  
Survey Methods ◽  
Functional Dependence ◽  
Generalized Additive Models ◽  
Substantial Reduction ◽  
Large Degree ◽  
Production Method ◽  
Additive Models ◽  
Sample Survey ◽  
Stochastic Variation

Generalized additive models (GAMs) are used to model spatial variation in egg density and increase the precision of biomass estimates from the daily egg production method. Application of GAMs to survey data from the western mackerel (Scomber scombrus) and horse mackerel (Trachurus trachurus) stocks result in a substantial reduction in coefficients of variation of egg abundance. In developing GAM methods for the daily egg production method, we generalize Pennington's method, in which presence-absence is modelled separately from nonzero observations, and use a new form of the bootstrap that accommodates clustered count data without requiring explicit modelling of the form of clustering. In addition to increasing estimation precision, the use of GAMs has several advantages over stratified sample survey methods. To a large degree they allow the data to determine the form of functional dependence of the response on explanatory variables; they accommodate a wide variety of forms of stochastic variation of the response; they provide maps of the predicted density within the survey area; they provide an objective means of interpolating into unsampled areas; and estimation does not assume random sampling with respect to location.

scholarly journals A revision of daily egg production estimation methods, with application to Atlanto-Iberian sardine. 2. Spatially and environmentally explicit estimates of egg production

2011 ◽  
Vol 68 (3) ◽  
pp. 528-536 ◽  
Author(s):  
Miguel Bernal ◽  
Yorgos Stratoudakis ◽  
Simon Wood ◽  
Leire Ibaibarriaga ◽  
Luis Valdés ◽  
...  
Keyword(s):  
Temporal Variability ◽  
Environmental Variables ◽  
Egg Production ◽  
Stock Assessment ◽  
Production Model ◽  
Estimation Methods ◽  
Statistical Framework ◽  
Spatio Temporal ◽  
The Relationship ◽  
Made In

Abstract Bernal, M., Stratoudakis, Y., Wood, S., Ibaibarriaga, L., Uriarte, A., Valdés, L., and Borchers, D. 2011. A revision of daily egg production estimation methods, with application to Atlanto-Iberian sardine. 2. Spatially and environmentally explicit estimates of egg production. – ICES Journal of Marine Science, 68: . A spatially and environmentally explicit egg production model is developed to accommodate a number of assumptions about the relationship between egg production and mortality and associated environmental variables. The general model was tested under different assumptions for Atlanto-Iberian sardine. It provides a flexible estimator of egg production, in which a range of assumptions and hypotheses can be tested in a structured manner within a well-defined statistical framework. Application of the model to Atlanto-Iberian sardine increased the precision of the egg production time-series, and allowed improvements to be made in understanding the spatio-temporal variability in egg production, as well as implications for ecology and stock assessment.

Using habitat association models to predict Alewife and Blueback Herring marine distributions and overlap with Atlantic Herring and Atlantic Mackerel: can incidental catches be reduced?

2015 ◽  
Vol 73 (7) ◽  
pp. 1912-1924 ◽  
Author(s):  
Sara M. Turner ◽  
John P. Manderson ◽  
David E. Richardson ◽  
John J. Hoey ◽  
Jonathan A. Hare
Keyword(s):  
Environmental Gradients ◽  
Generalized Additive Models ◽  
Habitat Associations ◽  
Additive Models ◽  
Clupea Harengus ◽  
Atlantic Herring ◽  
Alosa Pseudoharengus ◽  
Atlantic Mackerel ◽  
Blueback Herring ◽  
River Herring

Abstract Concern over the impacts of incidental catches of Alewife, Alosa pseudoharengus and Blueback Herring, A. aestivalis (collectively managed as ‘river herring’) in the commercial Atlantic Herring (Clupea harengus) and Atlantic Mackerel (Scomber scombrus) fisheries has resulted in the recent implementation of river herring incidental catch limits. These incidental catches are highly variable in frequency and magnitude, and the environmental conditions associated with these catches are poorly understood. We used generalized additive models (GAMs) to describe habitat associations of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel. Bottom temperature, bottom depth, bottom salinity, solar azimuth and elevation, and region of the Northeast U.S. continental shelf were all significant in the habitat models; GAMs explained 25.2, 16.9, 18.9, and 20.6% of the deviance observed for the presence/absence of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel. A subset of the data was omitted from the model and the probability of presence was compared with observations; 66–77% of observations were correctly predicted. The individual probabilities of presence were used to quantify and evaluate the accuracy of modelled overlap of Alewife and Blueback Herring with Atlantic Herring (68–72% correct predictions) and Alewife and Blueback Herring with Atlantic Mackerel (57–69% correct predictions). Our findings indicate that environmental gradients influence the distributions and overlap of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel, and with further testing and refinement these models could be developed into a tool to aid industry in reducing incidental catches of river herring.

scholarly journals Cycles, trends, and residual variation in the Iberian sardine (Sardina pilchardus) recruitment series and their relationship with the environment

2011 ◽  
Vol 69 (5) ◽  
pp. 739-750 ◽  
Author(s):  
M. Begoña Santos ◽  
Rafael González-Quirós ◽  
Isabel Riveiro ◽  
José M. Cabanas ◽  
Carmela Porteiro ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Generalized Additive Models ◽  
Causal Link ◽  
Additive Models ◽  
Dynamic Factor ◽  
Sardina Pilchardus ◽  
Residual Variation ◽  
Stock Biomass ◽  
Spawning Stock ◽  
Short Time

Abstract Santos, M. B., González-Quirós, R., Riveiro, I., Cabanas, J. M., Porteiro, C., and Pierce, G. J. 2012. Cycles, trends, and residual variation in the Iberian sardine (Sardina pilchardus) recruitment series and their relationship with the environment. – ICES Journal of Marine Science, 69: 739–750. Recruitment variability is an important component of the dynamics of Iberian sardine (Sardine pilchardus). Since 2006, poor recruitment has led to a decrease in stock biomass, the latest in a series of such crises for sardine fisheries. Understanding the mechanisms behind recruitment fluctuations has been the objective of many previous studies, and various relationships between recruitment and environmental variables have been proposed. However, such studies face several analytical challenges, including short time-series and autocorrelated data. A new analysis of empirical relationships with environmental series is presented, using statistical methods designed to cope with these issues, including dynamic factor analysis, generalized additive models, and mixed models. Relationships are identified between recruitment and global (number of sunspots), regional (NAOAutumn), and local [winter wind strength, sea surface temperature (SST), and upwelling] environmental variables. Separating these series into trend and noise components permitted further investigation of the nature of the relationships. Whereas the other three environmental variables were related to the trend in recruitment, SST was related to residual variation around the trend, providing stronger evidence for a causal link, possible mechanisms for which are discussed. After the removal of trend and cyclic components, residual variation in recruitment is also weakly related to the previous year's spawning-stock biomass.

A reanalysis of North Sea plaice spawning-stock biomass using the annual egg production method

2009 ◽  
Vol 66 (9) ◽  
pp. 1999-2011 ◽  
Author(s):  
Cindy J. G. van Damme ◽  
Loes J. Bolle ◽  
Clive J. Fox ◽  
Petter Fossum ◽  
Gerd Kraus ◽  
...  
Keyword(s):  
North Sea ◽  
Egg Production ◽  
Stock Assessment ◽  
Population Analysis ◽  
Spatial Dynamics ◽  
Production Method ◽  
Southern Bight ◽  
The North ◽  
Stock Biomass ◽  
Spawning Stock

Abstract van Damme, C. J. G., Bolle, L. J., Fox, C. J., Fossum, P., Kraus, G., Munk, P., Rohlf, N., Witthames, P. R., and Dickey-Collas, M. 2009. A reanalysis of North Sea plaice spawning-stock biomass using the annual egg production method. – ICES Journal of Marine Science, 66: 1999–2011. Uncertainty about the quality of current virtual population analysis-based stock assessment for North Sea plaice (Pleuronectes platessa) has led to various abundance indices. We compared biomass estimates from the annual egg production (AEP) method with current stock assessments based on catch-at-age to validate the current and historical perception of exploitation. The AEP method was also used to investigate the dynamics of the spatial components of plaice in the North Sea. We corrected for fecundity down-regulation and changes in sex ratio. Estimates from both methods were similar in trend and absolute biomass. On the Dogger Bank, there was a dramatic decline in biomass from 1948 and 1950 to 2004, and in the Southern Bight, the stock appeared to increase from 1987 and 1988 to 2004, although not reaching the historically high levels of 1948 or 1950. The timing of spawning of North Sea plaice does not appear to have changed throughout the period of high exploitation. We conclude that the AEP method is a useful way to hindcast the spatial dynamics of heavily exploited flatfish stocks.

scholarly journals Atlantic mackerel daily spawning dynamics and implications for batch fecundity estimations

2018 ◽  
Vol 75 (5) ◽  
pp. 1647-1654
Author(s):  
K Ganias ◽  
D Marmara ◽  
A Solla ◽  
D Garabana ◽  
R Dominguez-Petit
Keyword(s):  
Egg Production ◽  
Time Window ◽  
Production Method ◽  
Time Of Day ◽  
Batch Fecundity ◽  
Atlantic Mackerel ◽  
Spawning Frequency ◽  
Scomber Scombrus ◽  
Daily Spawning

Abstract The present study contributes to a better understanding of the daily spawning dynamics of southern NEA mackerel (Scomber scombrus) with implications for the estimation of batch fecundity. It shows that there is a time window during the day, mainly in the afternoon, during which the advanced oocyte mode in imminent spawners separates from the remaining, smaller oocytes. This synchronicity in the separation of the spawning batch amongst imminent spawners corroborates evidence for the existence of daily spawning synchronicity in the population. This is particularly important for applications of the daily egg production method, DEPM, because such pattern facilitates both the ageing of eggs for the estimation of the daily egg production at sea and the ageing of postovulatory follicles for the estimation of spawning frequency. For NEA mackerel, batch fecundity could only be measured when a clear hiatus was established between the spawning batch and the smaller oocytes. Hydrated females that do not show such hiatus would not be valid for batch fecundity measurements suggesting that the “hydrated oocytes method” is not fully applicable for this stock. Knowing the time of day at which the batch is separated, will facilitate the sampling of valid females for the estimation of batch fecundity.

scholarly journals From the Adriatic to Northern Norway—geographic differences in moult increment and moult probability of the European lobster (Homarus gammarus), across the natural range

2020 ◽  
Author(s):  
Matthew T Coleman ◽  
Anne-Lisbeth Agnalt ◽  
Jack Emmerson ◽  
Martial Laurens ◽  
Joanne S Porter ◽  
...  
Keyword(s):  
Fishery Management ◽  
Stock Assessment ◽  
Generalized Additive Models ◽  
Growth Patterns ◽  
Additive Models ◽  
Geographical Differences ◽  
Homarus Gammarus ◽  
Northern Latitudes ◽  
Natural Range ◽  
Geographic Differences

Abstract This study collated existing data on lobster moult increment from studies across the range of Homarus gammarus, together with new tagging data from Orkney, United Kingdom. Generalized additive models were used to investigate geographical differences in absolute moult increment and moult probability. Absolute moult increment was seen to differ significantly between regions and between sexes and showed a non-linear relationship with pre-moult size. Smaller absolute moult increments were observed at southern and northern latitudes with larger increments observed in the centre of the species range. Temperature was identified as a significant factor explaining differences in absolute moult increment between regions, consistent with there being a thermal optimum for growth for in H. gammarus. Moult and double moult probabilities decline with pre-moult size, with greatest probability of moulting occurring around day 250. Probability of double moulting increased with mean annual sea surface temperature. Regionally variable growth patterns, and localized adaptation to abiotic variables such as temperature, should therefore be taken into account when defining lobster stock assessment and fishery management areas.

scholarly journals Daily egg production of anchovy in European waters

2004 ◽  
Vol 61 (6) ◽  
pp. 944-958 ◽  
Author(s):  
Stylianos Somarakis ◽  
Isabel Palomera ◽  
Alberto Garcia ◽  
Luis Quintanilla ◽  
Constantin Koutsikopoulos ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Egg Production ◽  
Stock Assessment ◽  
Production Method ◽  
Bay Of Biscay ◽  
Spawning Habitat ◽  
Independent Information ◽  
Stock Biomass ◽  
Spawning Stock ◽  
The Mediterranean

Abstract Since the late 1980s, the Daily Egg Production Method (DEPM) has been applied to several anchovy stocks in European waters. DEPM surveys in the Bay of Biscay were well standardized and focused on providing fisheries-independent information for stock assessment purposes. Those targeting Mediterranean stocks were largely experimental and often opportunistic, with the main aim of developing and testing the method, rather than providing estimates of spawning stock biomass (SSB) for stock assessment. Consequently, the DEPM has been applied once, twice, or a maximum of three times in certain Mediterranean areas with no among-area standardization. Different techniques for several aspects of the method have been used in the Mediterranean, and the parameters estimated vary greatly among stocks and year of application. Evidence is provided that variability in biological production among sub-basins and/or years, a characteristic of Mediterranean Sea, may directly affect anchovy egg production. The daily specific fecundity of anchovy stocks can vary greatly among years, areas, or seasons in response to changing environmental and trophic regimes. When the correlation between regression-derived estimates of daily egg production and associated estimates of daily specific fecundity for anchovy in the Mediterranean, the Bay of Biscay, and upwelling areas are compared, a significant isometric relationship emerges for the Mediterranean and the Bay of Biscay, implying density-dependent use of spawning habitat. In upwelling areas, estimates of daily egg production are relatively high for a narrow range of generally low daily specific fecundities. There is a strong linear relationship between anchovy SSB and spawning area in European waters that does not differ significantly between the Bay of Biscay and the Mediterranean Sea.

Evaluating the use of the Daily Egg Production Method for stock assessment of blue mackerel, Scomber australasicus

2009 ◽  
Vol 60 (2) ◽  
pp. 112 ◽  
Author(s):  
T. M. Ward ◽  
P. J. Rogers ◽  
L. J. McLeay ◽  
R. McGarvey
Keyword(s):  
Egg Production ◽  
Early Stage ◽  
Stock Assessment ◽  
Production Method ◽  
Spawning Area ◽  
Eastern Australia ◽  
Genetic Techniques ◽  
Ovulatory Follicles ◽  
Improved Methods ◽  
Spawning Biomass

The present study evaluates the suitability of the Daily Egg Production Method (DEPM) for stock assessment of blue mackerel, Scomber australasicus and assesses methodological options for future applications. In southern Australia, estimates of mean daily egg production were higher for Californian Vertical Egg Tow (CalVET) nets than bongo nets, and in eastern Australia, were higher in October 2003 than July 2004. Estimates of spawning area for southern Australia were three times higher for bongo nets than CalVET nets. Similar estimates of spawning area were obtained using standard (manual) gridding and natural neighbour methods. Large samples and reliable estimates of all adult parameters were obtained for southern Australia. Relatively few spawning adults were collected off eastern Australia. Preliminary best estimates of spawning biomass for southern and eastern Australia were 56 228 t and 29 578 t, respectively, with most estimates within the ranges of 45 000–68 000 t and 20 000–40 000 t respectively. The DEPM is suitable for stock assessment of S. australasicus. Several technical refinements are required to enhance future applications, including: genetic techniques for identifying early stage eggs; a temperature–egg development key; improved methods for sampling adults off eastern Australia; and measurements of the degeneration rates of post-ovulatory follicles at several temperatures.

Improved estimation of age composition by accounting for spatiotemporal variability in somatic growth

2020 ◽  
Vol 77 (11) ◽  
pp. 1810-1821
Author(s):  
Giancarlo M. Correa ◽  
Lorenzo Ciannelli ◽  
Lewis A.K. Barnett ◽  
Stan Kotwicki ◽  
Claudio Fuentes
Keyword(s):  
Stock Assessment ◽  
Generalized Additive Models ◽  
Somatic Growth ◽  
Fish Population ◽  
Additive Models ◽  
Assessment Model ◽  
Spatiotemporal Variability ◽  
Age Composition ◽  
Growth Variability ◽  
Continuation Ratio

Age composition is defined as the proportion of a fish population belonging to each age class and is an informative input to stock assessment models. Variations in somatic growth rates may lead to larger errors in age composition estimates. To reduce this source of error, we compared the performance of four methods for estimating age compositions of a simulated fish population: two methods based on age–length keys (ALK, pooled and annual) and two model-based approaches (generalized additive models (GAMs) and continuation ratio logits (CRLs)). CRL was the most robust and precise method, followed by annual ALKs, particularly when significant growth variability was present. We applied these methods to survey age subsample data for Pacific cod (Gadus macrocephalus) in the eastern Bering Sea, estimating age compositions that were then incorporated in its stock assessment model. The model that included age compositions estimated by CRL displayed the highest consistency with other data in the model. CRL approach has utility for estimating age compositions employed in stock assessment models, especially when substantial variation in somatic growth is present.

Sign in / Sign up

Export Citation Format

Share Document