scholarly journals Estimation of the parameters of fish stock dynamics from catch-at-age data and indices of abundance: can natural and fishing mortality be separated?

2007 ◽  
Vol 64 (8) ◽  
pp. 1130-1142 ◽  
Author(s):  
Sondre Aanes ◽  
Steinar Engen ◽  
Bernt-Erik Sæther ◽  
Ronny Aanes
Keyword(s):  
Gadus Morhua ◽  
State Space Model ◽  
Population Projections ◽  
Quality Data ◽  
Fish Stock ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Absolute Size ◽  
Data Set ◽  
Long Time

Models for fluctuations in size of fish stocks must include parameters that describe expected dynamics, as well as stochastic influences. In addition, reliable population projections also require assessments about the uncertainties in estimates of vital parameters. Here we develop an age-structured model of population dynamics based on catch-at-age data and indices of abundance in which the natural and fishing mortality are separated in a Bayesian state–space model. Markov chain Monte Carlo methods are used to fit the model to the data. The model is fitted to a data set of 19 years for Northeast Arctic cod (Gadus morhua). By simulations of the fitted model we show that the model captures the dynamical pattern of natural mortality adequately, whereas the absolute size of natural mortality is difficult to estimate. Access to long time series of high-quality data are necessary for obtaining precise estimates of all the parameters in the model, but some parameters cannot be estimated without including some prior information. Nevertheless, our model demonstrates that temporal variability in natural mortality strongly affects perceived variability in stock sizes. Thus, using estimation procedures that neglect temporal fluctuations in natural mortality may therefore give biased estimates of fluctuations in fish stock sizes.

scholarly journals The effect of including length structure in yield-per-recruit estimates for northeast Arctic cod

2007 ◽  
Vol 64 (2) ◽  
pp. 357-368 ◽  
Author(s):  
Cecilie Kvamme ◽  
Bjarte Bogstad
Keyword(s):  
Alternative Model ◽  
Gadus Morhua ◽  
The Other ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Structured Model ◽  
Arctic Cod ◽  
Traditional Age ◽  
Size At Age ◽  
Yield Per Recruit

Abstract Kvamme, C., and Bogstad, B. 2007. The effect of including length structure in yield-per-recruit estimates for northeast Arctic cod. – ICES Journal of Marine Science, 64: 357–368. For northeast Arctic cod (Gadus morhua), traditional age-based estimates of yield per recruit (YPR) are compared with alternative, though comparable, YPR estimates calculated using an age–length-structured model. In the age–length-structured model, growth, fishing mortality, and natural mortality depend only on length, not on age. This model considers possible changes in size-at-age caused by, for example, a length-selective fishery, and therefore, by comparing the different YPR estimates, the importance of considering the stock's length structure can be evaluated. Length- and weight-at-age of stock and catches were influenced by exploitation pattern and pressure. Such changes are not considered in traditional estimates of YPR, for which weight-at-age is fixed and strictly speaking only representative for the current fishery. Consequently, traditional YPR estimates were somewhat higher than the age–length-based estimates for exploiting smaller fish than at present, and the other way round for exploiting larger fish. Both models indicated a gain in YPR for reducing just exploitation pressure (traditional YPR, 13%; alternative model, 20%) or both reducing exploitation pressure and postponing exploitation (traditional YPR, 23–31%; alternative model, 33–48%), compared with the current fishery.

scholarly journals “The Elephant in the Room”: Exploring Natural Mortality Uncertainty in Statistical Catch at Age Models

2020 ◽  
Vol 7 ◽  
Author(s):  
Alessandro Mannini ◽  
Cecilia Pinto ◽  
Christoph Konrad ◽  
Paraskevas Vasilakopoulos ◽  
Henning Winker
Keyword(s):  
Stock Assessment ◽  
Assessment Process ◽  
Sensitivity Analyses ◽  
Fish Stock ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Food And Agriculture ◽  
Stock Assessments ◽  
The Mediterranean ◽  
The Impact

The natural mortality rate (M) of a fish stock is typically highly influential on the outcome of age-structured stock assessment models, but at the same time extremely difficult to estimate. In data-limited stock assessments, M usually relies on a range of empirically or theoretically derived M estimates, which can vary vastly. This article aims at evaluating the impact of this variability in M using seven Mediterranean stocks as case studies of statistical catch-at-age assessments for information-limited fisheries. The two main bodies carrying out stock assessments in the Mediterranean and Black Seas are European Union’s Scientific Technical Economic Committee for Fisheries (STECF) and Food and Agriculture Organization’s General Fisheries Commission for the Mediterranean (GFCM). Current advice in terms of fishing mortality levels is based on a single “best” M assumption which is agreed by stock assessment expert working groups, but uncertainty about M is not taken into consideration. Our results demonstrate that not accounting for the uncertainty surrounding M during the assessment process can lead to strong underestimation or overestimation of fishing mortality, potentially biasing the management process. We recommend carrying out relevant sensitivity analyses to improve stock assessment and fisheries management in data-limited areas such as the Mediterranean basin.

In what direction should the fishing mortality target change when natural mortality increases within an assessment?

2016 ◽  
Vol 73 (3) ◽  
pp. 349-357 ◽  
Author(s):  
Christopher M. Legault ◽  
Michael C. Palmer
Keyword(s):  
Mortality Rate ◽  
Empirical Evidence ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Stock Assessment ◽  
Total Mortality ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Limanda Ferruginea ◽  
Trade Offs

Traditionally, the natural mortality rate (M) in a stock assessment is assumed to be constant. When M increases within an assessment, the question arises how to change the fishing mortality rate target (FTarget). Per recruit considerations lead to an increase in FTarget, while limiting total mortality leads to a decrease in FTarget. Application of either approach can result in nonsensical results. Short-term gains in yield associated with high FTarget values should be considered in light of potential losses in future yield if the high total mortality rate leads to a decrease in recruitment. Examples using yellowtail flounder (Limanda ferruginea) and Atlantic cod (Gadus morhua) are used to demonstrate that FTarget can change when M increases within an assessment and to illustrate the consequences of different FTarget values. When a change in M within an assessment is contemplated, first consider the amount and strength of empirical evidence to support the change. When the empirical evidence is not strong, we recommend using a constant M. If strong empirical evidence exists, we recommend estimating FTarget for a range of stock–recruitment relationships and evaluating the trade-offs between risk of overfishing and forgone yield.

Predicted extirpation of the dominant demersal fish in a large marine ecosystem: Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence

2008 ◽  
Vol 65 (11) ◽  
pp. 2315-2319 ◽  
Author(s):  
Douglas P. Swain ◽  
Ghislain A. Chouinard
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Marine Ecosystem ◽  
Demersal Fish ◽  
Population Projections ◽  
Individual Growth ◽  
Natural Mortality ◽  
Total Allowable Catch ◽  
Spawning Stock ◽  
Large Marine Ecosystem

Atlantic cod ( Gadus morhua ) was the dominant demersal fish and most important predator in the southern Gulf of St. Lawrence ecosystem as recently as the 1980s. However, productivity of southern Gulf cod has declined, and the population is no longer viable even in the absence of fishing. We conducted population projections taking into account uncertainty in current abundance-at-age and uncertainty or variability in each of the components of population productivity (i.e., rates of recruitment, individual growth, and adult natural mortality). We defined extirpation as a spawning stock biomass less than 1000 t (<0.3% of historical levels). Based on these projections, at its current level of productivity, this population is certain to be extirpated within 40 years in the absence of fishing and in 20 years with fishery removals at the level of the total allowable catch in 2007 and 2008 (2000 t). Elevated natural mortality of adult cod (M) is the main factor contributing to the low productivity of this stock. Because M appears to be increasing, our projections are likely overly optimistic.

Selection and estimation of sequential catch-at-age models

2012 ◽  
Vol 69 (11) ◽  
pp. 1760-1772 ◽  
Author(s):  
Gudmundur Gudmundsson ◽  
Thorvaldur Gunnlaugsson
Keyword(s):  
Measurement Errors ◽  
Gadus Morhua ◽  
Likelihood Function ◽  
Marginal Likelihood ◽  
Stock Assessment ◽  
Fish Stock ◽  
Natural Mortality ◽  
Selectivity Estimation ◽  
Time Series Modelling ◽  
Simplifying Assumptions

Fish stock assessment by catch-at-age and survey data is affected by many stochastic elements: measurement errors; sampling variations; natural variations in mortality, catchability and migrations; technological and social effects on fishing intensity and selectivity. Estimation of simulated models shows that the bias in estimation by linear approximation of the Kalman filter or automatic approximation of the marginal likelihood function is much smaller than the errors produced by the stochastic elements. In time series modelling, they are represented by residuals in the equations. Strong simplifying assumptions about these effects are common in catch-at-age analysis, but estimation of models for Icelandic cod ( Gadus morhua ) and pollock ( Pollachius virens , herein referred to as saithe) demonstrates that the relative importance of different random elements can vary greatly between stocks. These assumptions include exact catch-at-age measurements, no irregular migrations or variations in natural mortality, separable fishing mortality rates, and no permanent variations in survey catchability. Inappropriate simplificactions can have a strong effect on stock estimates. It is possible and important to test simplifying assumptions by comparison with more general models. Estimation of the magnitude of natural mortality is also examined.

Trends in Fishing Mortality Rate along with Errors in Natural Mortality Rate can cause Spurious Time Trends in Fish Stock Abundances Estimated by Virtual Population Analysis (VPA)

1989 ◽  
Vol 46 (12) ◽  
pp. 2129-2139 ◽  
Author(s):  
Michael F. Lapointe ◽  
Randall M. Peterman ◽  
Alec D. MacCall
Keyword(s):  
Mortality Rate ◽  
Time Trends ◽  
Biological Effects ◽  
Population Analysis ◽  
Fish Stock ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Management Actions ◽  
Virtual Population Analysis ◽  
Virtual Population

Many researchers have reported biases in estimates offish abundance reconstructed by virtual population analysis (VPA). We document that VPA can produce changing levels of bias through time, thereby creating spurious time trends in recruitment and stock biomass estimates. We generated catch data from empirically based simulations of nine fish populations, estimated abundances using VPA with a deliberately mis-specified natural mortality rate, M, and compared the estimates to the models' "true" abundances. A period of increasing fishing mortality rate, F, combined with an overestimate of M produced spurious decreasing time trends in estimated abundance and recruitment, even when the true time series of F was known. Analogously, an underestimate of M led to a spurious increasing time trend. Bias was increased by a higher true M, and (for a given total change in F) by a slower increase in F. Because field estimates of M are uncertain and trends in F are common, some apparent trends (or lack of them) in abundances reconstructed by VPA may be artifacts. Therefore, inferences about the results of past management actions and about physical or biological effects on variability in recruitment must be made cautiously when VPA estimates are used.

scholarly journals Handling Complex Missing Data Using Random Forest Approach for an Air Quality Monitoring Dataset: A Case Study of Kuwait Environmental Data (2012 to 2018)

2021 ◽  
Vol 18 (3) ◽  
pp. 1333
Author(s):  
Ahmad R. Alsaber ◽  
Jiazhu Pan ◽  
Adeeba Al-Hurban 
Keyword(s):  
Air Quality ◽  
Missing Data ◽  
Random Forest ◽  
Missing Values ◽  
Imputation Method ◽  
Environmental Data ◽  
Environmental Research ◽  
Quality Data ◽  
Data Set ◽  
Air Quality Data

In environmental research, missing data are often a challenge for statistical modeling. This paper addressed some advanced techniques to deal with missing values in a data set measuring air quality using a multiple imputation (MI) approach. MCAR, MAR, and NMAR missing data techniques are applied to the data set. Five missing data levels are considered: 5%, 10%, 20%, 30%, and 40%. The imputation method used in this paper is an iterative imputation method, missForest, which is related to the random forest approach. Air quality data sets were gathered from five monitoring stations in Kuwait, aggregated to a daily basis. Logarithm transformation was carried out for all pollutant data, in order to normalize their distributions and to minimize skewness. We found high levels of missing values for NO2 (18.4%), CO (18.5%), PM10 (57.4%), SO2 (19.0%), and O3 (18.2%) data. Climatological data (i.e., air temperature, relative humidity, wind direction, and wind speed) were used as control variables for better estimation. The results show that the MAR technique had the lowest RMSE and MAE. We conclude that MI using the missForest approach has a high level of accuracy in estimating missing values. MissForest had the lowest imputation error (RMSE and MAE) among the other imputation methods and, thus, can be considered to be appropriate for analyzing air quality data.

scholarly journals A Benchmark and Evaluation of Non-Rigid Structure from Motion

2020 ◽  
Author(s):  
Sebastian Hoppe Nesgaard Jensen ◽  
Mads Emil Brix Doest ◽  
Henrik Aanæs ◽  
Alessio Del Bue
Keyword(s):  
Computer Vision ◽  
Structure From Motion ◽  
State Of The Art ◽  
The State ◽  
Quality Data ◽  
Data Set ◽  
Rigid Structure ◽  
Public Data ◽  
3D Information ◽  
Further Development

AbstractNon-rigid structure from motion (nrsfm), is a long standing and central problem in computer vision and its solution is necessary for obtaining 3D information from multiple images when the scene is dynamic. A main issue regarding the further development of this important computer vision topic, is the lack of high quality data sets. We here address this issue by presenting a data set created for this purpose, which is made publicly available, and considerably larger than the previous state of the art. To validate the applicability of this data set, and provide an investigation into the state of the art of nrsfm, including potential directions forward, we here present a benchmark and a scrupulous evaluation using this data set. This benchmark evaluates 18 different methods with available code that reasonably spans the state of the art in sparse nrsfm. This new public data set and evaluation protocol will provide benchmark tools for further development in this challenging field.

Environmental influences on fish and shellfish production in the Northwest Atlantic

1994 ◽  
Vol 2 (1) ◽  
pp. 16-32 ◽  
Author(s):  
K.H. Mann ◽  
K.F. Drinkwater
Keyword(s):  
Environmental Factors ◽  
Gadus Morhua ◽  
Cold Water ◽  
Climatic Factors ◽  
Homarus Americanus ◽  
Fishing Mortality ◽  
Poor Growth ◽  
Northwest Atlantic ◽  
Grand Banks ◽  
Fish And Shellfish

Evidence is reviewed, linking physical oceanographic processes in the marine environment to changes in fish and shellfish stocks in the Northwest Atlantic. A case history study of the cod (Gadus morhua) stock of the northern Grand Banks and Labrador Shelf indicates a long slow amelioration of the environment between about 1945 and 1965, followed by a deterioration in the period 1965–1992. The most important environmental factors for the cod stocks appear to have been salinity and temperature. The trends can be traced back to climatic factors involving the Icelandic Low and the Azores–Bermuda High. When the atmospheric pressure difference in winter tended to be high, there was a progressive increase in the area of sea ice off Labrador and in the volume of cold water at depth. These factors have been shown to affect temperature and salinity conditions on the Grand Banks in spring and summer and are associated with poor growth and recruitment in the cod stocks. A similar case study of lobster (Homarus americanus) stocks indicates that temperature and river discharge are important environmental correlates, but neither can be shown to fully account for the recent trends in the stocks. Evidence is reviewed to show that physical environmental processes also influence recruitment and distribution of stocks of haddock, capelin, and squid. Some of the problems with correlational analysis are also discussed. It is recognized that factors other than the environment are influencing the stocks. Fishing mortality (detailed consideration of which is not included in this review) has clearly been important. Interactions between environmental factors and fishing mortality are probably of major importance.Key words: ocean environment, fish production, recruitment, northern cod, American lobster.

Natural mortality from poor condition in Atlantic cod (Gadus morhua)

2000 ◽  
Vol 57 (4) ◽  
pp. 826-836 ◽  
Author(s):  
Jean-Denis Dutil ◽  
Yvan Lambert
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Negative Impact ◽  
Fish Muscle ◽  
Early Summer ◽  
Wild Fish ◽  
Natural Mortality ◽  
Muscle Lactate ◽  
Lactate Dehydrogenase Activity ◽  
Poor Condition

The extent of energy depletion was assessed in Atlantic cod (Gadus morhua) in spring and early summer (1993-1995) to assess relationships between poor condition and natural mortality. Several indices of condition were compared in wild fish in the northern Gulf of St. Lawrence and in fish exposed to a prolonged period of starvation in laboratory experiments. Discriminant analyses classified only a small fraction of the wild fish as similar to cod that did not survive and a much larger fraction as similar to cod that survived starvation. This percentage increased from April to May and peaked in June 1993 and 1994. Condition factor and muscle somatic index allowed a clear distinction between live and dead fish. Muscle lactate dehydrogenase activity suggested that cod had experienced a period of negative growth early in 1993, 1994, and 1995. Fish classified as similar to starved individuals were characterized by a higher gonad to liver mass ratio than others. Reproduction may have a negative impact on survival not only in spring but also later into summer, as some individuals were found not to have recovered by late summer. This study shows that natural mortality from poor condition contributed to lower production in the early 1990s.

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