@article{Taylor2016,
archivePrefix = {arXiv},
arxivId = {http://dx.doi.org/10.6084/m9.figshare.4206561},
author = {Taylor, Marc H. and Mildenberger, Tobias K.},
doi = {10.6084/m9.figshare.4206561},
eprint = {/dx.doi.org/10.6084/m9.figshare.4206561},
primaryClass = {http:},
title = {{Extending ELEFAN in R. figshare. http://dx.doi.org/10.6084/m9.figshare.4206561}},
year = {2016}
}
@article{Taylor2015,
author = {Taylor, Marc H.},
title = {{Fishdynr}},
url = {https://github.com/marchtaylor/fishdynr},
year = {2015}
}
@article{Alverson1975,
author = {Alverson, D. L. and Carney., M. J.},
journal = {J. Cons. Int. Explor. Mer},
pages = {133--143},
title = {{A graphic review of the growth and decay of population cohorts}},
volume = {36},
year = {1975}
}
@article{Rose2010a,
abstract = {There is growing interest in models of marine ecosystems that deal with the effects of climate change through the higher trophic levels. Such end-to-end models combine physicochemical oceanographic descriptors and organisms ranging from microbes to higher-trophic-level (HTL) organisms, including humans, in a single modeling framework. The demand for such approaches arises from the need for quantitative tools for ecosystem-based management, particularly models that can deal with bottom-up and top-down controls that operate simultaneously and vary in time and space and that are capable of handling the multiple impacts expected under climate change. End-to-end models are now feasible because of improvements in the component submodels and the availability of sufficient computing power. We discuss nine issues related to the development of end-to-end models. These issues relate to formulation of the zooplankton submodel, melding of multiple temporal and spatial scales, acclimation and adaptation, behavioral movement, software and technology, model coupling, skill assessment, and interdisciplinary challenges. We urge restraint in using end-to-end models in a true forecasting mode until we know more about their performance. End-to-end models will challenge the available data and our ability to analyze and interpret complicated models that generate complex behavior. End-to-end modeling is in its early developmental stages and thus presents an opportunity to establish an open-access, community-based approach supported by a suite of true interdisciplinary efforts.},
author = {Rose, Kenneth a and Allen, J Icarus and Artioli, Yuri and Blackford, Jerry and Carlotti, Fran{\c{c}}ois and Cropp, Roger and Daewel, Ute and Edwards, Karen and Flynn, Kevin and Simeon, L and Megrey, Bernard and Moll, Andreas and Smith, S Lan and Smith, Chris and Solidoro, Cosimo and St, Michael},
doi = {10.1577/C09-059.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Rose et al/Rose et al. - 2010 - End-End Models for the Analysis of Marine Ecosystems Challenges, Issues and Next Steps.pdf:pdf},
issn = {1942-5120},
journal = {Marine and Coastal Fisheries},
pages = {115--130},
title = {{End-End Models for the Analysis of Marine Ecosystems: Challenges, Issues and Next Steps}},
volume = {2},
year = {2010}
}
@article{Sparre1989,
author = {Sparre, P},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Sparre/Sparre - 1989 - What is the optimum interval class size for length-frequency analysis.pdf:pdf},
journal = {Fishbyte},
keywords = {Length frequency theory},
number = {2},
pages = {23},
title = {{What is the optimum interval class size for length-frequency analysis?}},
volume = {7},
year = {1989}
}
@article{Nadon2015,
abstract = {The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable "average length in the exploited phase of the population ([Formula: see text])", estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30{\%} overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish (Scarus rubroviolaceus), and the gray snapper (Aprion virescens) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species (Lutjanus kasmira and Cephalopholis argus), had SPRs above the 30{\%} threshold.},
annote = {several weaknesses:

translate weigth to length and length to age for their models

underwater smapling and commercial fishieries sampling combined

growth, length, age parameters from other regions},
author = {Nadon, Marc O. and Ault, Jerald S. and Williams, Ivor D. and Smith, Steven G. and Dinardo, Gerard T.},
doi = {10.1371/journal.pone.0133960},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Nadon et al/journal.pone.0133960.pdf:pdf},
issn = {19326203},
journal = {PLoS ONE},
number = {8},
pages = {1--19},
pmid = {26267473},
title = {{Length-based assessment of coral reef fish populations in the main and Northwestern Hawaiian Islands}},
volume = {10},
year = {2015}
}
@article{Gayanilo1997a,
abstract = {This manual presents key concepts and methods found useful assessing the components of tropical and subtropical fish stocks, with emphasis on short- and medium-lived species of finfish and invertebrates (shrimps, squids, etc.) and on approaches based on the detailed analysis of length–frequency data. This account covers the preprocessing of length–frequency and ancillary data, growth estimation, mortality, gear selection, virtual population analysis and yield prediction. The manual is illustrated by means of computational examples, graphics and tabular printouts generated by the FiSAT software (FAO–ICLARM Stock Assessment Tools), and thus complements the FiSAT User's Manual.},
author = {Gayanilo, F C and Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gayanilo, Pauly/Gayanilo, Pauly - 1997 - FAO-ICLARM stock assessment tools Reference manual stock assessment tools Reference manual(2).pdf:pdf},
pages = {262},
title = {{FAO-ICLARM stock assessment tools Reference manual stock assessment tools Reference manual}},
year = {1997}
}
@article{Lassen2001,
abstract = {Virtual population analysis (VPA) is a widely used model for the analysis of fished populations. While there are many VPA techniques, they vary in the way they use data and fit the model rather than in the form of the model itself. This manual describes the common VPA model and the assumptions on which it is based, together with descriptions of associated diagnostic procedures and common reference points. More important, the manual describes the numerical techniques that can be used to fit the model based on weighted least-squares, which is the basis for the ADAPT approach. The techniques are described so that they are readily implemented in a spreadsheet. General methods and specific examples are given to enable readers to develop an approach suitable for their own data and fisheries. In addition to the printed document, a CD-ROM is provided that contains a series of exercises and examples. [From FAO website]},
author = {Lassen, Hans and Medley, Paul and Nations, Food and Agriculture Organization of the United and DANIDA},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Lassen et al/Lassen et al. - 2001 - Virtual Population Analysis.pdf:pdf},
isbn = {9789251045336},
journal = {A Practical Manual for Stock Assessment},
pages = {129},
title = {{Virtual Population Analysis}},
url = {http://books.google.com/books?id=kBe6PbIesmsC{\&}printsec=frontcover{\&}dq=intitle:VIRTUAL+POPULATION+ANALYSES+a+practical+manual+for+stock+assessment{\&}hl={\&}cd=1{\&}source=gbs{\_}api{\%}5Cnpapers3://publication/uuid/BB9A59C5-7213-4B88-B4DB-E6B81B9DB8D3},
year = {2001}
}
@article{Quenouille1956,
author = {Quenouille, M. H.},
journal = {Biometrika},
pages = {353--360},
title = {{Notes on bias in estimation}},
volume = {43},
year = {1956}
}
@article{ICES2012,
author = {ICES},
pages = {42},
title = {{ICES Implementation of Advice for Data-limited Stocks in 2012 in its 2012 Advice. In: ICES CM 2012/ACOM 68}},
year = {2012}
}
@article{Tesfaye2015,
author = {Tesfaye, Gashaw and Wolff, Matthias},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Tesfaye, Wolff/Tesfaye, Wolff - 2015 - Stock assessment of fishery target species in Lake Koka , Ethiopia.pdf:pdf},
keywords = {a means of livelihoods,exploitation rate,fisheries and are,for several million,growth,high,l opt,mega-spawners,mortality,optimum length,percentage to the global,size indicators,small-scale fisheries contribute a},
number = {September},
pages = {755--770},
title = {{Stock assessment of fishery target species in Lake Koka , Ethiopia}},
volume = {63},
year = {2015}
}
@article{Anderson2014,
abstract = {Simulation testing is an important approach to evaluating fishery stock assessment methods. In the last decade, the fisheries stock assessment modeling framework Stock Synthesis (SS3) has become widely used around the world. However, there lacks a generalized and scriptable framework for SS3 simulation testing. Here, we introduce ss3sim, an R package that facilitates reproducible, flexible, and rapid end-to-end simulation testing with SS3. ss3sim requires an existing SS3 model configuration along with plain-text control files describing alternative population dynamics, fishery properties, sampling scenarios, and assessment approaches. ss3sim then generates an underlying 'truth' from a specified operating model, samples from that truth, modifies and runs an estimation model, and synthesizes the results. The simulations can be run in parallel, reducing runtime, and the source code is free to be modified under an open-source MIT license. ss3sim is designed to explore structural differences between the underlying truth and assumptions of an estimation model, or between multiple estimation model configurations. For example, ss3sim can be used to answer questions about model misspecification, retrospective patterns, and the relative importance of different types of fisheries data. We demonstrate the software with an example, discuss how ss3sim complements other simulation software, and outline specific research questions that ss3sim could address.},
archivePrefix = {arXiv},
arxivId = {1312.6450},
author = {Anderson, Sean C. and Monnahan, Cole C. and Johnson, Kelli F. and Ono, Kotaro and Valero, Juan L.},
doi = {10.1371/journal.pone.0092725},
eprint = {1312.6450},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Anderson et al/Anderson et al. - 2014 - ss3sim An R package for fisheries stock assessment simulation with stock synthesis.pdf:pdf},
issn = {19326203},
journal = {PLoS ONE},
number = {4},
pages = {21--23},
pmid = {24699270},
title = {{ss3sim: An R package for fisheries stock assessment simulation with stock synthesis}},
volume = {9},
year = {2014}
}
@article{Taylor1958,
author = {Taylor, C. C.},
journal = {Journal du Conseil},
number = {3},
pages = {366--370},
title = {{Cod growth and temperature}},
volume = {23},
year = {1958}
}
@article{Tang2010a,
abstract = {Abstract  The estimation of gear selectivity is a critical issue in fishery stock assessment and management. Several methods have been developed for estimating gillnet selectivity, but they all have their limitations, such as inappropriate objective function in data fitting, lack of unique estimates due to the difficulty in finding global minima in minimization, biased estimates due to outliers, and estimations of selectivity being influenced by the predetermined selectivity functions. In this study, we develop a new algorithm that can overcome the above-mentioned problems in estimating the gillnet selectivity. The proposed algorithms include minimizing the sum of squared vertical distances between two adjacent points and minimizing the weighted sum of squared vertical distances between two adjacent points in the presence of outliers. According to the estimated gillnet selectivity curve, the selectivity function can also be determined. This study suggests that the proposed algorithm is not sensitive to outliers in selectivity data and improves on the previous methods in estimating gillnet selectivity and relative population density of fish when a gillnet is used as a sampling tool. We suggest the proposed approach be used in estimating gillnet selectivity.},
author = {Tang, Yanli and Huang, Liuyi and Ge, Changzi and Liang, Zhenlin and Sun, Peng},
doi = {10.1007/s00343-010-9256-2},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Tang et al/Tang et al. - 2010 - A new algorithm for estimating gillnet selectivity.pdf:pdf},
isbn = {0254-4059},
issn = {02544059},
journal = {Chinese Journal of Oceanology and Limnology},
keywords = {Kitahara method,algorithm,gillnet selectivity},
number = {2},
pages = {274--279},
title = {{A new algorithm for estimating gillnet selectivity}},
volume = {28},
year = {2010}
}
@article{Jørgensen2013,
abstract = {A stronger focus on natural mortality may be required to better understand contemporary changes in fish life histories and behaviour and their responses to anthropogenic drivers. Firstly, natural mortality is the selection under which fish evolved in the first place, so a theoretical understanding of effects of natural mortality alone is needed. Secondly, due to trade-offs, most organismal functions can only be achieved at some cost in terms of survival. Several trade-offs might need to be analysed simultaneously with effects on natural mortality being a common currency. Thirdly, there is scattered evidence that natural mortality has been increasing, some would say dramatically, in some fished stocks, which begs explanations. Fourthly, natural mortality most often implies transfer of mass and energy from one species to another, and therefore has foodweb and ecosystem consequences. We therefore analyse a model for evolution of fish life histories and behaviour, where state-dependent energy-allocation and growth strategies are found by optimization. Natural mortality is split into five different components, each specified as the outcome of individual traits and ecological trade-offs: a fixed baseline mortality; size-dependent predation; risk-dependent growth strategy; a fixed mortality when sexually mature; and mortality increasing with reproductive investment. The analysis is repeated with and without fishing. Each component of natural mortality has consequences for optimal life history strategies. Beyond earlier models, we show i) how the two types of reproductive mortality sometimes have similar and sometimes contrasting effects on life history evolution, ii) how ecosystem properties such as food availability and predation levels have stronger effects on optimal strategies than changing other mortality components, and iii) how expected changes in risk-dependent growth strategies are highly variable depending on the type of mortality changed. {\textcopyright} 2012 Elsevier B.V.},
author = {J{\o}rgensen, Christian and Holt, Rebecca E.},
doi = {10.1016/j.seares.2012.04.003},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/J{\o}rgensen, Holt/J{\o}rgensen, Holt - 2013 - Natural mortality Its ecology, how it shapes fish life histories, and why it may be increased by fishing.pdf:pdf},
isbn = {1385-1101},
issn = {13851101},
journal = {Journal of Sea Research},
keywords = {Adaptation,Behavioural ecology,Fishing-induced evolution,Life history evolution,Natural mortality,Trade-offs},
pages = {8--18},
publisher = {Elsevier B.V.},
title = {{Natural mortality: Its ecology, how it shapes fish life histories, and why it may be increased by fishing}},
url = {http://dx.doi.org/10.1016/j.seares.2012.04.003},
volume = {75},
year = {2013}
}
@article{Petriki2014a,
author = {Petriki, O. and Erzini, K. and Moutopoulos, D. K. and Bobori, D. C.},
doi = {10.1111/jai.12476},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Petriki et al/Petriki et al. - 2014 - Gillnet selectivity for freshwater fish species in three lentic systems of Greece.pdf:pdf},
issn = {01758659},
journal = {Journal of Applied Ichthyology},
number = {5},
pages = {1016--1027},
title = {{Gillnet selectivity for freshwater fish species in three lentic systems of Greece}},
url = {http://doi.wiley.com/10.1111/jai.12476},
volume = {30},
year = {2014}
}
@article{Hollowed2000a,
abstract = {We review the application of multispecies models as tools for evaluating impacts of fishing on marine communities. Four types of model are identified: descriptive multispecies, dynamic multispecies, aggregate system, and dynamic system models. The strengths and weaknesses of multispecies models and their ability to evaluate the causal mechanisms underlying shifts in production are examined. This comparison provides a basis for assessing the benefits of each modelling approach as a tool for evaluating impacts of fishing in marine ecosystems. Benefits of multispecies models include: improved estimates of natural mortality and recruitment; better understanding of spawner{\^{a}}€“recruit relationships and of variability in growth rates; alternative views on biological reference points; and a framework for evaluating ecosystem properties. Populations are regulated by competition (food limitation), predation, and environmental variability. Each factor may influence different life-history stages, locally or regionally. However, most multispecies models address only a subset of these factors, often aggregated over functionally different species or age groups. Models that incorporate the important interactions at specific stages and scales will be necessary if they are to continue to supplement the information provided by single-species models.},
author = {Hollowed, Anne B and Bax, Nicholas and Beamish, Richard and Collie, Jeremy and Fogarty, Michael and Livingston, Patricia and Pope, John and Rice, Jake C},
doi = {10.1006/jmsc.2000.0734},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hollowed/Hollowed et al. - 2000 - Are multispecies models an improvement on single-species models for measuring fishing impacts on marine ecosyst.pdf:pdf},
isbn = {1054-3139},
issn = {10543139},
journal = {ICES Journal of Marine Science: Journal du Conseil},
keywords = {ecosystem e ff ects,multispecies models,of fishing,predation,stock assess-},
number = {3},
pages = {707--719},
pmid = {1287},
title = {{Are multispecies models an improvement on single-species models for measuring fishing impacts on marine ecosystems?}},
url = {http://icesjms.oxfordjournals.org/content/57/3/707.abstract},
volume = {57},
year = {2000}
}
@article{He2011,
abstract = {The natural mortality rate (M) of fish varies with size and age, although it is often assumed to be constant in stock assessments. Misspecification of M may bias important assessment quantities. We simulated fishery data, using an age-based population model, and then conducted stock assessments on the simulated data. Results were compared to known values. Misspecification of M had a negligible effect on the estimation of relative stock depletion; however, misspecification of M had a large effect on the estimation of parameters describing the stock recruitment relationship, age-specific selectivity, and catchability. If high M occurs in juvenile and old fish, but is misspecified in the assessment model, virgin biomass and catchability are often poorly estimated. In addition, stock recruitment relationships are often very difficult to estimate, and steepness values are commonly estimated at the upper bound (1.0) and over-fishing limits tend to be biased low. Natural mortality can be estimated in assessment models if M is constant across ages or if selectivity is asymptotic. However if M is higher in old fish and selectivity is dome-shaped, M and the selectivity cannot both be adequately estimated because of strong interactions between M and selectivity.},
author = {He, Xi and Ralston, Stephen and MacCall, Alec D.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/He, Ralston, MacCall/He, Ralston, MacCall - 2011 - Interactions of age-dependent mortality and selectivity functions in age-based stock assessment models.pdf:pdf},
isbn = {0090-0656},
issn = {00900656},
journal = {Fishery Bulletin},
number = {2},
pages = {198--216},
title = {{Interactions of age-dependent mortality and selectivity functions in age-based stock assessment models}},
volume = {109},
year = {2011}
}
@article{Kunzmann1991,
author = {Kunzmann, K R and Wegener, M},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kunzmann, Wegener/Kunzmann, Wegener - 1991 - Berichte aus dem Institut f{\"{u}}r Raumplanung.pdf:pdf},
number = {177},
title = {{Berichte aus dem Institut f{\"{u}}r Raumplanung}},
volume = {2},
year = {1991}
}
@article{Giannetto2014a,
abstract = {Key-words: growth, gill-net selectivity, alien species, euthrophic lake, fisheries management The analysis of catch selectivity of fishing equipment is a crucial step for the management of alien species in freshwater ecosystems. Roach Ru-tilus rutilus was introduced in many waterways in Italy often becoming the dominant species of the fish community and it is now considered po-tential pest. In Piediluco lake the species was first found in 2004 and its abundance has increased at a level that creates concern for the other fish species present in the lake. The growth of R. rutilus and the selectivity of gill-nets on its population were examined in Piediluco lake by analysing the selectivity of gill-nets of different mesh size. Sampling was conducted from January 2011 to October 2012 by means of gill-nets of different-sized mesh (8, 10, 12.5, 15.5, 19.5, 24, 28, 35, 45 and 55 mm). The results showed that R. rutilus in Piediluco lake had a growth faster and higher than in many other lake environments. The results of gill-nets selectivity gave important information to design a plan to control this species and confirmed that the use of suitable fishing techniques could be useful to manage the population of this alien species in Piediluco lake as well as in other similar environments. R{\'{E}}SUM{\'{E}} S{\'{e}}lectivit{\'{e}} en taille des filets maillants et croissance du gardon Rutilus rutilus (Linnaeus, 1758), une esp{\`{e}}ce exotique au lac de Piediluco (Italie) Mots-cl{\'{e}}s : croissance, s{\'{e}}lectivit{\'{e}}, filet maillant, esp{\`{e}}ce exotique, lac eutrophe, gestion des p{\^{e}}ches L'analyse de la s{\'{e}}lectivit{\'{e}} des captures du mat{\'{e}}riel de p{\^{e}}che est une {\'{e}}tape cruciale pour la gestion des esp{\`{e}}ces exotiques dans les {\'{e}}cosyst{\`{e}}mes d'eau douce. Le gardon Rutilus rutilus a {\'{e}}t{\'{e}} introduit dans de nombreux cours d'eau en Italie, devenant souvent l'esp{\`{e}}ce dominante de la communaut{\'{e}} de pois-sons et il est maintenant consid{\'{e}}r{\'{e}} comme nuisible potentiel. Dans le lac de Piediluco l'esp{\`{e}}ce a {\'{e}}t{\'{e}} d{\'{e}}couverte en 2004 et son abondance a augment{\'{e}} {\`{a}} un niveau qui suscite des inqui{\'{e}}tudes pour les autres esp{\`{e}}ces de poissons pr{\'{e}}sents dans le lac. La croissance de R. rutilus et la s{\'{e}}lectivit{\'{e}} des filets maillants sur la population ont {\'{e}}t{\'{e}} examin{\'{e}}es au lac de Piediluco par l'ana-lyse de la s{\'{e}}lectivit{\'{e}} des filets maillants de maillages diff{\'{e}}rents. L'{\'{e}}chantillon-nage a {\'{e}}t{\'{e}} effectu{\'{e}} de janvier 2011 {\`{a}} octobre 2012 au moyen de filets maillants de diff{\'{e}}rentes mailles (8, 10, 12.5, 15.5, 19.5, 24, 28, 35, 45 et 55 mm). Les r{\'{e}}sultats ont montr{\'{e}} que R. rutilus du lac de Piediluco a connu une croissance},
author = {Giannetto, D and Carosi, A and Ghetti, L and Pompei, L and Viali, P and Lorenzoni, M},
doi = {10.1051/kmae/2014001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Giannetto et al/Giannetto et al. - 2014 - Size selectivity of gill-nets and growth of roach Rutilus rutilus (Linnaeus, 1758) an alien species in Pied(2).pdf:pdf},
issn = {1961-9502},
journal = {Knowledge and Management of Aquatic Ecosystems},
pages = {1--13},
title = {{Size selectivity of gill-nets and growth of roach Rutilus rutilus (Linnaeus, 1758) an alien species in Piediluco lake (Italy)}},
url = {http://www.kmae-journal.org},
volume = {413},
year = {2014}
}
@article{Brock1962,
author = {Brock, VE},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Brock/Brock - 1962 - On the nature of the selective fishing action of longline gear.pdf:pdf},
title = {{On the nature of the selective fishing action of longline gear}},
url = {http://scholarspace.manoa.hawaii.edu/handle/10125/5972},
year = {1962}
}
@article{Christensen1992a,
author = {Christensen, V and Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Christensen, Pauly/Christensen, Pauly - 1992 - ECOPATH II - a software for balancing steady-state ecosystem models and calculating network characteristics.pdf:pdf;:Users/tobiasmildenberger/Documents/Mendeley Desktop/Christensen, Pauly/Christensen, Pauly - 1992 - ECOPATH II - a software for balancing steady-state ecosystem models and calculating network characteristi(2).pdf:pdf},
journal = {Science},
number = {681},
pages = {169--185},
title = {{ECOPATH II - a software for balancing steady-state ecosystem models and calculating network characteristics}},
volume = {61},
year = {1992}
}
@article{Yalcn-Ozdilek2013,
abstract = {Pseudorasbora parva (Temminck and Schlegel, 1846) is widely distributed in rivers and lakes of Turkey owing to accidental introductions. Turkey is rich in biodiversity of freshwater fish and has a high level of endemicity of native ichthyofauna, which is vulnerable to such introductions. The Geling{\"{u}}ll{\"{u}} Reservoir located on the Kızılırmak drainage in Central Anatolia has rich ichthyofauna with native and introduced fish species, including endemic species. The contents of the foregut of P. parva samples collected between Summer 2003 and Summer 2005 were examined. Seasonal and ontogenetic changes in feeding intensity were determined. P. parva mainly feeds on zooplankton such as Cladocera, Copepoda, and Rotifera. Members of the Bacillariophyta and Cyanobacteria were identified in high proportions in the foregut contents of P. parva particularly during summer. The feeding traits of this invasive fish may have an influence on the establishment of a successful population in Geling{\"{u}}ll{\"{u}} reservoir.},
author = {Yal{\c{c}}ın-{\"{O}}zdilek, Ş{\"{u}}kran and Kırankaya, Şerife G{\"{u}}ls{\"{u}}n and Ekmek{\c{c}}i, Fitnat G{\"{u}}ler},
doi = {10.4194/1303-2712-v13},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Yal{\c{c}}ın-{\"{O}}zdilek, Kırankaya, Ekmek{\c{c}}i/Yal{\c{c}}ın-{\"{O}}zdilek, Kırankaya, Ekmek{\c{c}}i - 2013 - Feeding ecology of the topmouth gudgeon Pseudorasbora parva (Temminck and Schlegel, 1.pdf:pdf},
isbn = {1303-2712},
issn = {13032712},
journal = {Turkish Journal of Fisheries and Aquatic Sciences},
keywords = {1846,bireylerinin beslenme ekolojisi,de geling{\"{u}}ll{\"{u}} barajı,ecology,feeding,geling{\"{u}}ll{\"{u}},invasive,nda yaşayan pseudorasbora parva,pseudorasbora parva,temminck and schlegel,t{\"{u}}rkiye},
number = {January},
pages = {87--94},
pmid = {2009353409},
title = {{Feeding ecology of the topmouth gudgeon Pseudorasbora parva (Temminck and Schlegel, 1846) in the Geling{\"{u}}ll{\"{u}} Reservoir, Turkey}},
volume = {13},
year = {2013}
}
@article{Huse2000,
abstract = {A full-scale fishing experiment on north-east Arctic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus), involving a trawler, a longliner and a gillnetter was conducted in order to determine how the length distributions and life history parameters of the catches were affected by gear type. Relative selectivity was analysed for catches taken when the boats fished simultaneously in the same area, and when the skippers were allowed to fish under conditions as close as possible to commercial operation. Trawl and longline-caught cod had similar length distributions, but cod caught by trawl were on average 2.3 cm smaller than longline-caught cod. Cod caught by longline had a lower condition factor and length at age. The longliner caught smaller haddock than the trawler when the boats fished in the same area. When the skippers were allowed to change fishing ground, the mean length of cod increased in the trawl catches and became larger than the mean length in the longline catches. The mean length of haddock in the longline catches increased by 2.8 cm and became larger than that of the trawl catches. Gillnet catches consisted almost solely of large cod. Mean length of gillnet caught fish in 186 mm nets decreased from 86.2 cm to 82.3 cm even if the boat did not change area. Separate selectivity experiments for trawl and gillnet were conducted, and the parameters for the mesh selection are presented. To find the functional form of the longline selectivity we used relative catch proportion in each 5 cm length-group for longline compared to trawl and gillnet, whose selectivities were assumed to be known. When compared to that of the gillnet, the plots indicate that the longline selectivity curve takes the form of a unimodal distribution. When longline catches was compared to trawl catches none of the suggested models seemed to fit, and to conclude anything about the form of the longline selection curve is not possible. (C) 2000 International Council for the Exploration of the Sea.},
author = {Huse, I and L{\o}kkeborg, S and Soldal, a V},
doi = {10.1006/jmsc.2000.0813},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Huse, L{\o}kkeborg, Soldal/Huse, L{\o}kkeborg, Soldal - 2000 - Relative selectivity in trawl, longline and gillnet fisheries for cod and haddock.pdf:pdf},
isbn = {1054-3139},
issn = {10543139},
journal = {ICES Journal of Marine Science},
keywords = {CATCH,FISHING GEAR,FUNCTIONAL FORM,IMPACT,LINE,MODEL,SIZE-SELECTIVITY,catch-comparisons,gillnet,longline,selectivity,trawl},
number = {4},
pages = {1271--1282},
title = {{Relative selectivity in trawl, longline and gillnet fisheries for cod and haddock}},
volume = {57},
year = {2000}
}
@article{Barr2010,
author = {Barr, Mehdat A Abdel and El-Sayed, Abdel Fattaqh M and Osman, Amany M.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Barr, El-Sayed, Osman/Barr, El-Sayed, Osman - 2010 - The use of per recruit models for stock assessment and management of greasy grouper Epinephelus tauvina i.pdf:pdf},
issn = {19853718},
journal = {Tropical Life Sciences Research},
keywords = {Arabian Gulf,Epinephelus tauvina,Per recruit models},
number = {1},
pages = {83--90},
title = {{The use of per recruit models for stock assessment and management of greasy grouper Epinephelus tauvina in the Arabian Gulf waters off Qatar}},
volume = {21},
year = {2010}
}
@article{Marjomaki2015,
author = {Marjom{\"{a}}ki, Timo J. and Paloniemi, Marko and Keskinen, Tapio and Kuha, Jonna and Karjalainen, Juha},
doi = {10.2174/1874401X01508010013},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Marjom{\"{a}}ki et al/Marjom{\"{a}}ki et al. - 2015 - Empirical Estimation of Accumulation-Induced Change in Gill Net Catchability Mind the Observation Errors.pdf:pdf},
issn = {1874-401X},
journal = {The Open Fish Science Journal},
keywords = {accumulation,bias,catchability,error in variables,saturation},
number = {1},
pages = {13--22},
title = {{Empirical Estimation of Accumulation-Induced Change in Gill Net Catchability: Mind the Observation Errors}},
url = {http://benthamopen.com/ABSTRACT/TOFISHSJ-8-13},
volume = {8},
year = {2015}
}
@article{Thordarson,
author = {Thordarson, Gudmundur and Bj{\"{o}}rnsson, H{\"{o}}skuldur},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Thordarson, Bj{\"{o}}rnsson/Thordarson, Bj{\"{o}}rnsson - Unknown - Are F max and F 0 . 1 really illusive as fisheries reference points.pdf:pdf},
journal = {Fisheries (Bethesda)},
number = {30},
pages = {1--10},
title = {{Are F max and F 0 . 1 really illusive as fisheries reference points ?}}
}
@article{M??ller2015,
abstract = {Oxygen isotope (??18O) records of incrementally banded marine calcifiers provide high-resolution information about modern and past environmental conditions. However, given their biological origin, these records are often distorted by ontogenetic and seasonal growth pattern. To evaluate their reliability, many studies correlate skeletal ??18O records with instrumentally measured time series of environmental conditions using a variety of methods to recalculate their temporal framework. Lacking consistency and a limited traceability of many temporal alignment methods underline the need for standardized and flexible method for the temporal alignment of sclerochronological records. Here, two methods for the temporal alignment of sclerochronological data and their application on measured oxygen isotope signatures of a fish otolith and a marine bivalve shell are presented and compared. The first method is a flexible approach using a linear interpolation between carefully selected temporal reference points for recalculating ontogenetic growth effects with an optional extension accounting for seasonal growth oscillations. The second approach uses the seasonally-oscillating Von Bertalanffy growth function parameterized based on the oxygen isotope record to reconstruct the underlying growth model and reconstruct thereby its temporal framework. Using these methods, we re-align ??18O-based water temperature records of a Carlarius heudelotii otolith and a Venus crebrisulca shell with measured sea surface temperature time series and compare the resulting correlation as well as the different underlying growth models. Our results show that both methods represent useful tools for the temporal alignment of sclerochronological records. However, underlying growth models strongly differ depending on the temporal alignment method and the parameters used for the reconstruction of the temporal framework. This underlines the importance of a careful selection of a particular alignment method depending on the complexity of distortion due to seasonal and ontogenetic growth trajectories. Moreover, we show that both organisms represent reliable paleoenvironmental archives providing sub-seasonally resolved water temperature records.},
author = {M??ller, Peter and Taylor, Marc H. and Klicpera, Andr?? and Wu, Henry C. and Michel, Julien and Westphal, Hildegard},
doi = {10.1016/j.palaeo.2015.09.032},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Mller et al/Mller et al. - 2015 - Food for thought Mathematical approaches for the conversion of high-resolution sclerochronological oxygen isotope.pdf:pdf},
issn = {00310182},
journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
keywords = {Bivalve,Growth model,Otolith,Sclerochronology,Temporal alignment,Von Bertalanffy growth function},
pages = {763--776},
publisher = {Elsevier B.V.},
title = {{Food for thought: Mathematical approaches for the conversion of high-resolution sclerochronological oxygen isotope records into sub-annually resolved time series}},
url = {http://dx.doi.org/10.1016/j.palaeo.2015.09.032},
volume = {440},
year = {2015}
}
@article{Package2015,
author = {Package, Type and Kell, Author Laurence and Evalu-, Management Strategy},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Package, Kell, Evalu-/Package, Kell, Evalu- - 2015 - Package ‘ kobe '.pdf:pdf},
title = {{Package ‘ kobe '}},
year = {2015}
}
@article{Heery2009,
abstract = {Abstract Length frequency data are a central component of many statistical age-structured models, which are used widely to conduct fisheries stock assessments and produce estimates of stock status for management. However, these data can be biased due to systematic errors during the sampling process. This study examined how bias in length frequency data affected stock status estimates from an age-structured assessment model and subsequent prescribed management actions. A simulation approach was used to test the effect of two different scenarios of bias on assessment results. Populations were simulated based on life history parameters for three different serranid species in the southeastern United States and followed a trajectory that increased and then decreased over time. From these simulated populations, fishery-dependent length frequency data were generated and then altered to represent different types of systematic sampling error. Data that were biased towards larger fish had a considerable effect on the age-structured assessment model, producing more-optimistic estimates of stock status, which tended to support management actions that would not adequately protect stocks from overfishing. This may be particularly problematic for longer-lived species and for stocks that have been depleted well below their original population size. Stock status estimates were much less affected by data that contained a higher frequency of small fish, although this type of biased length frequency information could support unnecessarily stringent management actions in the most extreme cases. The results of this study suggest that error and possible bias in length frequency data should be thoroughly considered when selecting an appropriate modeling approach for fisheries stock assessment.},
author = {Heery, Eliza C and Berkson, Jim},
doi = {10.1577/t07-226.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Heery, Berkson/Heery - Length bias.pdf:pdf},
isbn = {0002-8487},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
number = {1},
pages = {218--232},
title = {{Systematic errors in length frequency data and their effect on age-structured stock assessment models and management}},
url = {http://www.tandfonline.com/doi/abs/10.1577/T07-226.1},
volume = {138},
year = {2009}
}
@article{Zhang2010,
abstract = {A biomass-based length-cohort analysis (LCA) was examined for its performance in estimating total stock biomass and fishing mortality (F) for a population in equilibrium. We compared two LCA methods-(1) a numbers-based LCA that relies on catch numbers at length as input data and (2) a new biomass-based LCA that relies on catch biomass at length-by applying both to simulated data that generally followed characteristics of Pacific chub mackerel Scomber japonicus in Korean waters. We investigated the effects of using two length aggregation methods, two data simulation methods, and three expressions of weight growth (i.e., exponential growth over the length increment of the analysis, arithmetic mean growth, and geometric mean growth). Biomass and F were estimated from the new model and compared with those estimated from the numbers-based LCA model. A sensitivity analysis was performed to understand which aspect of the model parameters controlled the results. Sensitivity to estimates of terminal F was also examined. Results of the analysis showed that the allometric power coefficient beta was the most important model parameter and that sensitivity of biomass-based LCA to terminal F was similar to that of numbers-based LCA. Monte Carlo simulation was used to evaluate the equilibrium assumption and to calculate confidence intervals for biomass estimates. We applied the biomass-based LCA model to data for northern rock sole Lepidopsetta polyxystra in the eastern Bering Sea. A comparison of biomass-based LCA population biomass estimates with northern rock sole research survey biomass estimates showed good agreement between the two types of estimates. The biomass-based LCA described in this study is unique in that it incorporates growth explicitly into the estimation procedure, which can be useful under data-deficient situations when simple length composition data and estimates of total catch biomass from just one sampling year are the only available data.},
author = {Zhang, Chang Ik and Megrey, Bernard a.},
doi = {10.1577/T09-041.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Zhang, Megrey/Zhang, Megrey - 2010 - A Simple Biomass-Based Length-Cohort Analysis for Estimating Biomass and Fishing Mortality.pdf:pdf},
isbn = {0002-8487},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
number = {3},
pages = {911--924},
title = {{A Simple Biomass-Based Length-Cohort Analysis for Estimating Biomass and Fishing Mortality}},
volume = {139},
year = {2010}
}
@article{Yoshimoto1993,
author = {Yoshimoto, Stacey S and Clarke, Raymond P},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Yoshimoto, Clarke/Yoshimoto, Clarke - 1993 - Comparing Dynamic Versions.pdf:pdf},
number = {5},
title = {{Comparing Dynamic Versions}},
year = {1993}
}
@article{Millar1992c,
abstract = {A conditional maximum likelihood model is used to estimate the size-selectivity of trawls, gillnets, and hooks when the data are obtained by simultaneous fishing with meshes or hooks of different size and/or shape. Size-selectivity is expressed here by the selection curve, r(l), the probability that a fish of length 1, if contacting the gear, will be retained (caught). In many selectivity studies r(l) is fitted either by eye, by heuristic means, or by improper application of generalized linear models. Then it is not possible to make legitimate statistical inference about r(l), or about assessments of the state of the fishery if those assessments use r(l). It is shown here that by conditioning on the total catch, selectivity data can be modeled as binary data, or polytomous data on interval scales. Application of the model to trawl and hook data demonstrates that selection curves can be fitted using generalized linear models, which may require nonstandard link functions or link functions with parameter},
author = {Millar, Russell B.},
doi = {10.1080/01621459.1992.10476250},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Millar/Millar - 1992 - Estimating the size-selectivity of fishing gear by conditioning on the total catch(2).pdf:pdf},
isbn = {0162-1459},
issn = {0162-1459},
journal = {Journal of the American Statistical Association},
keywords = {conditional maximum likelihood,fishing gear,generalized linear models,logistic curves,poisson totals},
number = {420},
pages = {962--968},
title = {{Estimating the size-selectivity of fishing gear by conditioning on the total catch}},
url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1992.10476250},
volume = {87},
year = {1992}
}
@article{Vetter1988,
abstract = {The instantaneous rate of natural mortality (M) is an important but poorly quantified parameter in most mathematical models of fish stock dynamics. This report reviews methods used commonly to estimate M for fish stocks. sensitivity of some common fishery models to values chosen for M. and evidence refuting the common assumption that a constant value can be an adequate approximation of M within single stocks. With the exception of simple surplus production models (e.g.. Schaefer 1954; Pella and Tomlinson 1969) all mathematical models of fish stock dy-namics include as a parameter the instantaneous rate of natural mortality (M). The models do not require explicitly any particular form for M; it can be constant or can vary in any imaginable form. But because natural mortality has proved extremely difficult to measure directly. M is as-sumed almost universally to be some constant specific to whatever stock is being modeled. This is particularly true for analyses of commercial fish stocks. which often require estimates of M only for the postrecruit ages. Decreases in natural mortality with increasing age during egg and postlarval stages are so dramatic compared to ap-parent changes during postrecruitment ages (e.g.. Cushing 1975) or compared to differences be-tween different sexes. collection sites. seasons, years. cohorts. or stocks within species. that vari-ations in M during these later (postrecruitment) ages are often assumed negligible.},
author = {Vetter, E. F.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Vetter/Vetter - 1988 - Estimation of natural mortality in fish stocks a review.pdf:pdf},
isbn = {0090-0656},
issn = {00900656},
journal = {Fishery Bulletin},
number = {1},
pages = {25--43},
title = {{Estimation of natural mortality in fish stocks: a review}},
volume = {86},
year = {1988}
}
@misc{Pauly1980,
abstract = {A compilation of values for the exponential coefficient of natural mortality (M) is given for 175 different stocks of fish distributed in 84 species, both freshwater and marine, and ranging from polar to tropical waters. Values of L oc (/''/, em), W{\~{}}(g, fresh weight), K (l/year) and T eC, mean annual water temperature) were attributed to each value of M, and the 175 sets of values plotted such that: t) tog M {\~{}} -0'2107 - 0{\textperiodcentered}0824 tog Woo + 0 {\textperiodcentered}6757 tog K + 0 A627 log T and 2) logM = -0-0066 - 0{\textperiodcentered}279 log Lex, + 0{\textperiodcentered}6543 log K + 0-4634 log T The multiple correlation coefficients are for 1) n {\textperiodcentered}845, and for 2) 0 {\textperiodcentered}84 7, while the critical value (171 d.f.) isO{\textperiodcentered}275 (for P = 0{\textperiodcentered}01). All slopes are significantly :f-. U (for P ::: 0{\textperiodcentered}001). The standard deviation of estimates or log M are for 1) 0{\textperiodcentered}247, lind for 2) 0{\textperiodcentered}245. The equations provide highly reliable estimates of M for any given fish stock, given the values of Woc or L'f.) and K of the von Bertalanffy growth formula, and an estimate of the mean water temperature in which the stock in question lives. Only two groups have values of M generally differing from those obtained through the proposed equations: the Clupeidae, with generally lower and the polar fishes with generally higher values. Correction factors are given for both groups. Potential appli- cations of the findings to population dynamics are discussed together with some ecological implications. Introduction},
author = {Pauly, Daniel},
booktitle = {Journal du Conseil},
doi = {10.1093/icesjms/39.2.175},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly/Pauly - 1980 - On the Interrelationships Between Natural Mortality, Growth Parameters, and Mean Environmental Temperature in 175 Fish St.pdf:pdf},
isbn = {0020-6466},
issn = {1054-3139},
number = {2},
pages = {175--192},
pmid = {2380},
title = {{On the Interrelationships Between Natural Mortality, Growth Parameters, and Mean Environmental Temperature in 175 Fish Stocks}},
url = {http://icesjms.oxfordjournals.org/content/39/2/175.short},
volume = {39},
year = {1980}
}
@article{GayaniloJr1996,
author = {{Gayanilo Jr}, F. C. and Sparre, P. and Pauly, P.},
title = {{FiSAT: FAO-ICLARM stock assessment tools. User's manual. FAO.}},
year = {1996}
}
@article{Kvamme2007,
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.},
author = {Kvamme, Cecilie and Bogstad, Bjarte},
doi = {10.1093/icesjms/fsl027},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kvamme, Bogstad/Kvamme, Bogstad - 2007 - The effect of including length structure in yield-per-recruit estimates for northeast Arctic cod.pdf:pdf},
issn = {10543139},
journal = {ICES Journal of Marine Science},
keywords = {Age-length-structured population model,Age-structured population model,Gadget,Gadus morhua,Yield per recruit},
number = {2},
pages = {357--368},
title = {{The effect of including length structure in yield-per-recruit estimates for northeast Arctic cod}},
volume = {64},
year = {2007}
}
@article{Kokkalis2015,
abstract = {For stocks which are considered "data-poor" no knowledge exist about growth, mortality or recruitment. The only available information is from catches. Here we examine the ability to assess the level of exploitation of a data-poor stock based only on information of the size of individuals in catches. The model is a formulation of the classic Beverton-Holt theory in terms of size where stock parameters describing growth, natural mortality, recruitment, etc. are determined from life-history invariants. A simulation study was used to compare the reliability of assessments performed under different information availability scenarios, from data-limited, where none of the parameters are known beforehand, to different degrees of information availability cases where one or more parameters are known. If no parameters are known it is possible to correctly assess whether the fishing mortality is below F{\textless}inf{\textgreater}msy{\textless}/inf{\textgreater} in more than 60{\%} of the cases, and almost always correctly assess whether a stock is subject to overfishing. Adding information about age, i.e., assuming that growth rate and asymptotic size are known, does not improve the estimation. Only knowledge of the ratio between mortality and growth led to a considerable improvement in the assessment. Overall, the simulation study demonstrates that it may be possible to classify a data-poor stock as undergoing over- or under-fishing, while the exact status, i.e., how much the fishing mortality is above or below F{\textless}inf{\textgreater}msy{\textless}/inf{\textgreater}, can only be assessed with a substantial uncertainty. Limitations of the approach are discussed.},
author = {Kokkalis, Alexandros and Thygesen, Uffe H. and Nielsen, Anders and Andersen, Ken H.},
doi = {10.1016/j.fishres.2014.10.007},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kokkalis et al/Kokkalis 2014 Limits to the reliability of size-based fishing status estimation for data-poor stocks.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Beverton-Holt life history invariants,Data-poor assessment,Parameter estimation,Size structure},
number = {May 2016},
pages = {4--11},
title = {{Limits to the reliability of size-based fishing status estimation for data-poor stocks}},
volume = {171},
year = {2015}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - WF-14.pdf.pdf:pdf},
title = {{WF-14.pdf}}
}
@article{Gedamke2006,
abstract = {The Beverton-Holt length-based mortality estimator has received widespread use primarily due to its applicability in data-limited situations. The mean length of animals that are fully vulnerable to the sampling gear can be used to estimate total mortality from basic growth parameters and a known length at first capture. This method requires equilibrium conditions because the mean length of a population will change only gradually after a change in mortality. In this study, we derive the transitional behavior of the mean length statistic for use in nonequilibrium conditions. We investigate conditions affecting the reliability of the Beverton-Holt results and then develop a new procedure that allows a series of mortality rates to be estimated from mean length data representing nonequilibrium conditions in multiple years. We then examine an assessment of goosefish Lophius americanus that was criticized for its use of the Beverton-Holt estimator under nonequilibrium conditions. Using data from the 1963-2002 National Marine Fisheries Service annual fall groundfish surveys off the northeastern United States and assuming a single change in total mortality, we used the maximum likelihood method to estimate that the total mortality of goosefish in the southern assessment region increased from 0.31 to 0.60 per year in 1977. Estimates of the new mortality rate made three or more years after the change were relatively stable and only ranged from 0.55 to 0.71 per year, while estimates from the standard Beverton-Holt approach ranged from 0.37 to 1.1 per year. The results for goosefish in the northern assessment region showed that total mortality changed from 0.14 to 0.29 per year in 1978 and then to 0.55 per year in 1987. The new nonequilibrium estimator allows a change in mortality to be characterized reliably several years faster than would occur with the use of the Beverton-Holt estimator.},
author = {Gedamke, Todd and Hoenig, John M.},
doi = {10.1577/T05-153.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gedamke, Hoenig/Gedamke, Hoenig - 2006 - Estimating Mortality from Mean Length Data in Nonequilibrium Situations, with Application to the Assessment of.pdf:pdf},
isbn = {0002-8487$\backslash$n1548-8659},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
number = {2},
pages = {476--487},
title = {{Estimating Mortality from Mean Length Data in Nonequilibrium Situations, with Application to the Assessment of Goosefish}},
volume = {135},
year = {2006}
}
@article{Reis1992,
abstract = {The object of this study was to determine a method of estimating the selectivity of gill nets for which catch data are available for only a few mesh sizes. A model inferring retention from girth measurements of fish and mesh dimension, but which is independent of catch data, resulted in wide selectivity curves, which could not be used to predict the mesh size which would most efficiently catch fish in a particular length range. Methods utilising observed frequency distributions of the ratio between mesh perimeter and fish length or girth provided good fits between the catch and selectivity curves for the mesh sizes most used in a bass (Dicentrarchus labrax) fishery. The role and usefulness of these selectivity models in the management of gill-net fisheries is discussed.},
author = {Reis, E.G. and Pawson, M.G.},
doi = {10.1016/0165-7836(92)90025-O},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Reis, Pawson/Reis, Pawson - 1992 - Determination of gill-net selectivity for bass (Dicentrarchus labrax L.) using commercial catch data.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
number = {2},
pages = {173--187},
title = {{Determination of gill-net selectivity for bass (Dicentrarchus labrax L.) using commercial catch data}},
volume = {13},
year = {1992}
}
@article{Prager1994,
abstract = {Surplus-production models, because of their simplicity and relatively undemanding data needs, are attractive tools for many stock assessments. This paper reviews the logistic production model, starting with the basic differential equation and continuing with a description of the model development without the equilibrium assumption. It then describes several extensions, including ''tuning'' the model to a biomass index; partitioning fishing mortality by gear, time, or area; and making projections. Computation of confidence intervals on quantities of interest (e.g. maximum sustainable yield (MSY), effort at MSY, level of stock biomass relative to the optimum level) can be done through boot-strapping, and the bootstrap can also be used to construct nonparametric tests of hypotheses about changes in catchability. To fit the model, an algorithm that uses a forward solution of the population equations can be implemented on a small computer. An example of the utility of surplus-production models (illustrating several of these extensions) is given. The example is loosely based on swordfish (Xiphias gladius) in the North Atlantic Ocean, but is not intended to describe the actual status of that stock.},
author = {Prager, M. H.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prager/Prager - 1994 - A suite of extensions to a nonequilibrium surplus-production model.pdf:pdf},
isbn = {0090-0656},
issn = {00900656},
journal = {Fishery Bulletin},
number = {2},
pages = {374--389},
title = {{A suite of extensions to a nonequilibrium surplus-production model}},
volume = {92},
year = {1994}
}
@article{Statistics1921,
abstract = {Bulletins are designed to assess and interpret current knowledge in scientific fields pertinent to Canadian fisheries and aquatic environments. Re- cent numbers in this series are listed at the back of this Bulletin.},
author = {Statistics, Biological},
doi = {10.1038/108070b0},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Statistics/Statistics - 1921 - Biological Statistics.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
number = {2706},
pages = {70--70},
title = {{Biological Statistics}},
volume = {108},
year = {1921}
}
@misc{Somers1988a,
author = {Somers, Ian F.},
booktitle = {Fishbyte},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Somers/Somers - 1988 - On A Seasonally Oscillating Growth Function.pdf:pdf},
pages = {8--11},
title = {{On A Seasonally Oscillating Growth Function}},
volume = {6},
year = {1988}
}
@article{CemalDincer2008,
abstract = {The mesh selectivity of multifilament gillnets for red mullet (Mullus barbatus) was investigated using four different stretched mesh sizes (32, 36, 40 and 44 mm). Experimental fishing operations were carried out in Trabzon (Turkey) coasts of the Black Sea in springtime between 2002 and 2003. Selectivity on M. barbatus was assessed using the SELECT method, implemented in the PASGEAR software. Five different functional models; normal location, normal scale, gamma, log-normal and bi-model were used to fit the selectivity curve to the catch data. It was shown that the bi-model function was the hest to fit the data. For the selectivity curves oil the bi-model, the optimum lengths (100{\%} retention probability for the 32, 36, 40 and 44 mill mesh sizes) were obtained as 14.24 cm, 16.02 cm, 17.8 cm, and 19.58 cm, respectively. Considering the minimum allowable landing size (13 cm) 36 mm was found the most adequate mesh for exploiting the red mullet as it evidenced more conservative approach towards fishing management.},
author = {{Cemal Din{\c{c}}er}, a. and Bahar, Mustafa},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Cemal Din{\c{c}}er, Bahar/Cemal Din{\c{c}}er, Bahar - 2008 - Multifilament Gillnet selectivity for the Red Mullet (Mullus barbatus) in the Eastern Black Sea Coast of T.pdf:pdf},
isbn = {1303-2712},
issn = {13032712},
journal = {Turkish Journal of Fisheries and Aquatic Sciences},
keywords = {Black Sea,Gillnet,Mesh selectivity,Red mullet,SELECT method},
number = {2},
pages = {355--359},
title = {{Multifilament Gillnet selectivity for the Red Mullet (Mullus barbatus) in the Eastern Black Sea Coast of Turkey, Trabzon}},
volume = {8},
year = {2008}
}
@book{Beddington1983,
author = {Beddington, J.R. and Cooke, J.G.},
booktitle = {FAO Fish. Tech. Pap.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Beddington, Cooke/Beddington, Cooke - 1983 - The potential yield of fish stocks.pdf:pdf},
isbn = {9251014175},
pages = {47},
title = {{The potential yield of fish stocks}},
volume = {242},
year = {1983}
}
@article{Gulland1973a,
abstract = {The sustainable yield, or maximum sustainable yield, has been used to provide, on an objective scientific basis, target figures for the catches to be taken from a heavily exploited stock that is under regulation. The simple concept of sustainable yield does not, however, provide a completely adequate guide when the biological system is complex. Certain other quantities-the replacement yield, the sustainable yield from a stock in equilibrium, the maintainable yield, and the catch for desired harvesting rate-are defined which correspond more closely to the biological reality. One or other of these will provide a better guide for management, depending on the nature of the divergence from the simple model. In whale populations the major divergence is the lag between changes in adult stock and changes in recruitment; replacement yield or maintainable yield are the most useful. In many fish stocks, fluctuations in year-class strength are more important: catch for desired harvesting rate may be better. Various fishing research organizations are concerned with the setting of annual catch quotas or other measures for the management of the resources which are their responsibility. Agreement on the level of these quotas is more easily reached if they are determined by objec­ tive scientific criteria. Apart from the continuing difficulty in making precise assessments con­ cerning any wild animals, this guidance is difficult to provide without some agreed basis on how the "correct" catch should be calculated. At present there is not a single theoretical model for determining this catch that combines all the desirable features of (a) being readily understandable (at least in general outline) to the decision makers, (b) describing and predict­ ing in a realistic manner, and to an acceptable degree of precision the events in every fish stock to which it may need to be applied, and (c) capable of being applied to a specific fishery without great demands in data and analysis. The models associated with Schaefer (1954) on the one hand and with Ricker (1958) and Beverton and Holt (1957) (in the simple form when no account is taken of fishery-induced changes in recruitment) on the other fail, for many important fisheries, to satisfy the second Scientific advice on catch levels - ResearchGate. Available from: http://www.researchgate.net/publication/216900194{\_}Scientific{\_}advice{\_}on{\_}catch{\_}levels [accessed Aug 13, 2015].},
author = {Gulland, J.a. and Boerema, L.K.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gulland, Boerema/Gulland, Boerema - 1973 - Scientific advice on catch levels.pdf:pdf},
journal = {Fishery Bulletin},
number = {2},
pages = {325--335},
title = {{Scientific advice on catch levels}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Scientific+advice+on+catch+levels{\#}0},
volume = {71},
year = {1973}
}
@article{Trust2016,
author = {Trust, Biometrika},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Trust/Trust - 2016 - Biometrika Trust A Comparison of Estimates of Natural Mortality from Fish Tagging Experiments Author ( s ) G . M . Leigh.pdf:pdf},
number = {2},
pages = {347--353},
title = {{Biometrika Trust A Comparison of Estimates of Natural Mortality from Fish Tagging Experiments Author ( s ): G . M . Leigh Published by : Oxford University Press on behalf of Biometrika Trust Stable URL : http://www.jstor.org/stable/2336183 REFERENCES Link}},
volume = {75},
year = {2016}
}
@article{Garc??a-Berthou2012,
author = {Garc??a-Berthou, Emili and Carmona-Catot, Gerard and Merciai, Roberto and Ogle, Derek H.},
doi = {10.1007/s11160-012-9262-x},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Garca-Berthou et al/Garca-Berthou et al. - 2012 - A technical note on seasonal growth models.pdf:pdf},
isbn = {1116001292},
issn = {09603166},
journal = {Reviews in Fish Biology and Fisheries},
keywords = {Fishery models,Seasonality,Somers' (1988) growth model,Temperature,von Bertalanffy growth function},
number = {3},
pages = {635--640},
title = {{A technical note on seasonal growth models}},
volume = {22},
year = {2012}
}
@article{Millar1997b,
abstract = {The log-linear modelling capabilities of existing statistical software permit a generaliz- ation of Holt's indirect estimation method by allowing several different selection curve models to be fitted to catch data from an arbitrary number of mesh sizes. This also facilitates the use of formal inferential procedures such as model selection, assessment of relative fishing powers, estimation of standard errors, and permits inclusion of knowledge regarding the shape of the population length distribution. This methodol- ogy is equally applicable to estimation of hook selectivity},
author = {Millar, R. B. and Holst, R.},
doi = {10.1006/jmsc.1996.0196},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Millar, Holst/Millar, Holst - 1997 - Estimation of gillnet and hook selectivity using log-linear models(2).pdf:pdf},
isbn = {1054-3139},
issn = {10543139},
journal = {ICES Journal of Marine Science},
keywords = {accepted 12 september 1996,b,count data,curves,department of mathematics and,gillnet selectivity,hook selectivity,log-linear models,maximum likelihood,millar,o,p,r,received 30 december 1995,select method,selection,statistics,university of otago},
number = {1963},
pages = {471--477},
title = {{Estimation of gillnet and hook selectivity using log-linear models}},
url = {http://icesjms.oxfordjournals.org/content/54/3/471.short},
volume = {54},
year = {1997}
}
@misc{Hilderbrand2000,
author = {Hilderbrand, RH},
booktitle = {Transactions of the American},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hilderbrand/Hilderbrand - 2000 - Mortality.pdf.pdf:pdf},
title = {{Mortality.pdf}},
url = {http://www.tandfonline.com/doi/abs/10.1577/1548-8659(2000)129{\%}3C1160:MPOSRC{\%}3E2.0.CO;2},
year = {2000}
}
@article{Park1978,
abstract = {The von Bertalanffy model of body growth is inappropriate for organisms whose growth is restricted to a seasonal period because it assumes that growth rate is invariant with time. Incorporation of a time-varying coefficient significantly improves the capability of the von Bertalanffy equation to describe changing body size of both the bivalve mollusc Macotna baltllica in San Francisco Bay and the flathead sole, Hippoglossoides elassodon, in Washington state. This simple modification of the von Bertalanffy model should offer improved predictions of body growth for a variety of other aquatic animals.},
author = {Park, Menlo},
doi = {10.1139/f78-231},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Park/Park - 1978 - A von Bertalanffy Growth Mode! with a Seasonally Varying Coeflicient.pdf:pdf},
issn = {0015-296X},
journal = {Journal of the Fisheries Research Board of Canada},
keywords = {1479 1482,1978,35,a n d f,a von bertalanffy growth,appliquer b des,bertalanffy,board can,c loern,corporelle de von bertalanffy,e,fish,growth model,growth rate,h,j,le modkle de croissance,macorna halthica,model with a seasonally,n ichols,ne peut s,res,varying coeficient},
number = {55229},
pages = {1479--1482},
pmid = {439},
title = {{A von Bertalanffy Growth Mode! with a Seasonally Varying Coeflicient}},
url = {http://sfbay.wr.usgs.gov/publications/pdf/cloern{\_}1978{\_}bertalanffy.pdf},
volume = {35},
year = {1978}
}
@misc{Wolff1984,
author = {Wolff, Matthias},
booktitle = {ICLARM Newsletter},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Wolff/Wolff - 1984 - Early Setback for Scallop Culture in Peru.pdf:pdf},
title = {{Early Setback for Scallop Culture in Peru}},
year = {1984}
}
@article{Selectivity1963a,
author = {Selectivity, T H E and Fishing, O F},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Selectivity, Fishing/Selectivity, Fishing - 1963 - International commission.pdf:pdf},
title = {{International commission}},
volume = {2},
year = {1963}
}
@article{Xiang2013,
abstract = {Many problems in statistics, finance, biology, pharmacology, physics, mathematics, economics, and chemistry involve determination of the global minimum of multidimensional functions. R packages for different stochastic methods such as genetic algorithms and differential evolution have been developed and successfully used in the R community. Based on Tsallis statistics, the R package GenSA was developed for generalized simulated annealing to process complicated non-linear objective functions with a large number of local minima. In this paper we provide a brief introduction to the R package and demonstrate its utility by solving a non-convex portfolio optimization problem in finance and the Thomson problem in physics. GenSA is useful and can serve as a complementary tool to, rather than a replacement for, other widely used R packages for optimization.},
author = {Xiang, Y and Gubian, Sylvain and Suomela, Brian and Hoeng, Julia},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Xiang et al/Xiang et al. - 2013 - Generalized simulated annealing for global optimization the GenSA Package.pdf:pdf},
isbn = {2073-4859},
issn = {20734859},
journal = {R Journal},
number = {June},
pages = {13--28},
title = {{Generalized simulated annealing for global optimization: the GenSA Package}},
url = {http://rjournal.github.io/archive/2013-1/xiang-gubian-suomela-etal.pdf},
volume = {5},
year = {2013}
}
@article{Faife2003,
author = {Faife, J R},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Faife/Faife - 2003 - Effect of mesh size and twine type on gillnet selectivity of cod (Gadus morhua) in Icelandic coastal waters.pdf:pdf},
pages = {23},
title = {{Effect of mesh size and twine type on gillnet selectivity of cod (Gadus morhua) in Icelandic coastal waters}},
year = {2003}
}
@article{Gaertner2010,
author = {Gaertner, Daniel and Chassot, Emmanuel and Fonteneau, Alain and Hallier, Jean Pierre and Marsac, Francis},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gaertner et al/Gaertner et al. - 2010 - Estimate of the Non-Linear Growth Rate of Yellowfin Tuna ( Thunnus Albacares ) in the Atlantic and Indian Ocean.pdf:pdf},
journal = {Collect. Vol. Sci. Pap. ICCAT},
number = {2},
pages = {683--694},
title = {{Estimate of the Non-Linear Growth Rate of Yellowfin Tuna ( Thunnus Albacares ) in the Atlantic and Indian Oceans From Tagging Data}},
volume = {65},
year = {2010}
}
@article{Pauly1985b,
author = {Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly/Pauly - 1985 - On improving operation and use of the ELEFAN programs. Part I avoiding 'drift' of k towards low values.pdf:pdf},
journal = {Fishbyte},
number = {3},
pages = {13--14},
title = {{On improving operation and use of the ELEFAN programs. Part I: avoiding 'drift' of k towards low values}},
volume = {3},
year = {1985}
}
@article{Grundlagen2000,
author = {Grundlagen, I},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Grundlagen/Grundlagen - 2000 - Zur Mathematik des tierischen Wachstums.pdf:pdf},
number = {1978},
pages = {499--526},
title = {{Zur Mathematik des tierischen Wachstums}},
volume = {526},
year = {2000}
}
@article{Sparre1998b,
author = {Sparre, P. and Venema, SC},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Sparre, Venema/Sparre, Venema - 1998 - Introduction to Tropical Fish Stock Assessment(2).pdf:pdf},
journal = {FAO Technical Paper},
title = {{Introduction to Tropical Fish Stock Assessment}},
year = {1998}
}
@article{Jude2002,
author = {Jude, D. and Neethiselvan, N. and Gopalakrishnan, P. and Sugumar, G.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Jude et al/Jude et al. - 2002 - Gill net selectivity studies for fishing frigate tuna, Auxis thazard Lacepede (PerciformesScombridae) in Thoothukku.pdf:pdf},
issn = {03795136},
journal = {Indian Journal of Marine Sciences},
keywords = {Auxis thazard,Big meshed drift gill nets,Commercially significant length group,Frigate tuna,Length at first maturity],Mesh size},
number = {4},
pages = {329--333},
title = {{Gill net selectivity studies for fishing frigate tuna, Auxis thazard Lacepede (Perciformes/Scombridae) in Thoothukkudi(Tuticorin)waters, southeast coast of India}},
volume = {31},
year = {2002}
}
@article{Vakily1992,
abstract = {An analysis of shell microstructure of A. granosa and P, virids experimentally cultured in coastal waters of Thailand revealed that the formation of growth lines was closely related to tidal periodicity. It is concluded that growth lines are formed when the bivalves react with shell closure to reduced water flow, the degree of sensitivity being species- specific. The application of the methodology to tropical bivalves seems, however, not recommendable, given the rather demanding preparative work and the large degree of uncertainty involved in the interpretation of observed growth lines. Fitting of growth data from the culture experiments to the von Bertalanffy growth function (VBGF) showed large variations of the single growth parameters, but little variance in the resulting growth index, {\$}', supporting the perception of @' being a species- specific parameter. This concept was further investigated by computing the index @' from growth parameters of 190 bivalve stocks compiled or computed from the literature. It was shown that 4' is usually narrowly distributed around a species-specific mean. Use of @' for growth comparison between different genera is generally limited because of the different shell shape, which strongly influences Q'. However, mytilids with their relative uniform shell shape displayed a linear increase of @' with environmental water temperature, suggesting that bivalves tend to grow larger in warm waters. This is in contrast to general observations in fish, and is explained by the difference in energy demand for the precipitation of calcium carbonate from seawater.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Vakily, J M},
doi = {10.1007/s13398-014-0173-7.2},
eprint = {arXiv:1011.1669v3},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Vakily/Vakily - 1992 - Determination and Comparison of Bivalve Growth, with Emphasis on Thailand and Other Tropical Areas.pdf:pdf},
isbn = {36},
issn = {13514180},
journal = {ICLARM Technical Reports 36},
keywords = {bivalve,determination,growth},
pages = {1--121},
pmid = {15991970},
title = {{Determination and Comparison of Bivalve Growth, with Emphasis on Thailand and Other Tropical Areas}},
year = {1992}
}
@article{Millar1999,
author = {Millar, RB and Fryer, RJ},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Millar, Fryer/Millar, Fryer - 1999 - Estimating the size-selection curves of towed gears, traps, nets and hooks.pdf:pdf},
journal = {Reviews in Fish Biology and Fisheries},
pages = {89--116},
title = {{Estimating the size-selection curves of towed gears, traps, nets and hooks}},
url = {http://link.springer.com/article/10.1023/A:1008838220001},
year = {1999}
}
@book{Næsje2004,
abstract = {Objective The objective of this report is to provide baseline infor- mation about the fish resources in the Namibian part of the Kwando River to form the biological foundation for recommendations for a sustainable management of the fish resources. Based on fish survey data from the period 1997-1999, the fish resources are described through studies of species diversity, relative impor- tance of the different species, life history parameters, catch per unit effort and gill net selectivity. Methods Fish were collected at ten stations with survey gill nets (multi-filament, 22–150 mm stretched mesh size) and six other sampling methods, such as seine nets, cast nets, electrofishing apparatus and rotenone, which are collectively called ”other gears” in this report. The gill nets were used to survey open, deep-water habitats ({\textgreater} 1 m) in the main stream near the shore and deep backwater areas with some aquatic vegetation. The other gears targeted mainly small species and juve- niles of long-lived species in shallow, vegetated and rocky habitats. Surveys were carried out in the spring in 1997 and 1998 and in the autumn in 1997, 1998 and 1999. A total of 2756 fish were caught; 1172 with gill nets and 1584 with other gears. The most important species in the catches were identified by using an index of rela- tive importance (IRI), which is a measure of the rela- tive abundance or commonness of the species based on number and weight of individuals in the catches, as well as their frequency of occurrence. Eighteen of the most important species collected were selected for a more detailed analysis of life history and gill net selectivity. Results A total of 48 fish species were recorded during the surveys, in addition to unidentified Synodontis species. Due to difficulties with the taxonomic classification in the Synodontis spp. group, these species have been pooled, except the easily recognised Synodontis nigro- maculatus. Four Synodontis species have previously been listed for the Kwando River. The fish families represented with the highest number of species were the Cyprinidae and the Cichlidae, with 10 and 15 spe- cies, respectively. 5 Thirty species were caught in the gill nets (exclud- ing Syno dontis spp.). The ten most important spe- cies contributed to 97 {\%} of the total IRI. The three most important species (Marcusenius macrolepidotus, Hydrocynus vittatus and Petrocephalus catostoma) con- tributed to 56 {\%} of the total IRI. The Mormyridae family was the most important family in the gill net catches (50 {\%} of the total IRI). The Characidae fam- ily was also important in the gill net catches (31 {\%}), whereas the Cichlidae family constituted only a small part (5 {\%}). Thirty-eight species were caught with other gears than gill nets (no Synodontis spp. was caught with the other gears). The ten most important species contributed to 98 {\%} of the total IRI. The three most important species (Pharyngochromis acuticeps, Pseudocrenilabrus philander and Micralestes acutidens) contributed to 68 {\%} of the total IRI. In contrast to the gill net catches, the Cichlidae was the most important family in the catches with other gears, according to IRI (66 {\%}). The number of species caught was higher for tthe catches with other gears than with gill nets, which is attrib- uted to the flexibility of the other gears, and that a much wider range of habitats was sampled. The body length of the fish caught was up to 66 cm. The modal length of fish caught in gill nets was 8.0- 8.9 cm, whereas for fish caught with the other gears 3.0-3.9 cm. Thus, larger fish were caught with gill nets than with the other gears, and this was true both for the species combined and for individual species. Twelve of the species caught had a maximum body length of 6 cm or smaller. The 18 species selected for a more detailed data anal- ysis, contributed to 92 {\%} of the gill net catches and 90 {\%} of the catches with the other gears, according to IRI. These species represented a large variation in biology, distribution and sizes. Of the selected spe- cies, seven species had a minimum length at maturity smaller than 10 cm, three species between 11 and 20 cm and four species larger than 20 cm. The minimum length at maturity was larger than or similar to thesmallest fish caught with gill nets in all the selected species, except for both sexes of Pseudocrenilabrus philander. Comparison among rivers The results from the surveys in the Kwando River were compared with previous studies in the Zambezi/},
author = {N{\ae}sje, Tor F and Hay, Clinton J and Nickanor, Nande and Koekemoer, Johan H and Strand, Rita and Thorstad, Eva B},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/N{\ae}sje et al/N{\ae}sje et al. - 2004 - Fish populations , gill net catches and gill net selectivity in the Kwando River , Namibia Fish populations , gil.pdf:pdf},
isbn = {8242614806},
number = {7485},
pages = {64 pp},
title = {{Fish populations , gill net catches and gill net selectivity in the Kwando River , Namibia Fish populations , gill net catches and gill net selectivity in the Kwando River , Namibia}},
url = {http://www.nina.no/archive/nina/PppBasePdf/projectReport/027.pdf},
year = {2004}
}
@article{Gulland1992a,
abstract = {Rome, FAO. 1992. 100p This document reviews the several fish stock assessment methods based on length-frequency analysis. Emphasis is placed on sampling and collection of length-frequency data, to the estimation of population parameters such as growth, mortality and recruitment and the estimation of catch selectivity. Attention is given to the conversion of length to age using age-length keys, slicing length-frequency composition, and using modes. It reviews long-and short-term effects of changes in selection and fishing mortality, and discusses methods for long-term assessments and for short-term projections. The manual gives several examples of the most common methods used and stresses the advantages of using personal computers and the most recent software for data processing and analysis.},
author = {Gulland, J A and Rosenberg, A A},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gulland, Rosenberg/Gulland, Rosenberg - 1992 - A review of length-based approaches to assessing fish stocks.pdf:pdf},
isbn = {92-5-103121-5},
journal = {FAO Fisheries Technical Paper},
number = {323},
title = {{A review of length-based approaches to assessing fish stocks}},
year = {1992}
}
@article{Ogle2016,
author = {Ogle, D.H.},
title = {{FSA: Fisheries Stock Analysis. R package version 0.8.9.}},
year = {2016}
}
@article{Hansen1997a,
abstract = {Gillnet selectivity for lake trout (Salvelinus namaycush) was estimated indirectly from catches in nets of 102-, 114-, 127-, 140-, and 152-mm stretch measure. Mesh selectivity was modeled as a nonlinear response surface that describes changes in the mean, standard deviation, and skewness of fish lengths across mesh sizes. Gillnet selectivity for lake trout was described by five parameters that explained 88{\%} of the variation in wedged and entangled catches, 81{\%} of the variation in wedged catches, and 82{\%} of the variation in entangled catches. Combined catches of wedged and entangled lake trout were therefore described more parsimoniously than separate catches of wedged and entangled lake trout. Peak selectivity of wedged and entangled fish increased from 588 to 663 mm total length as mesh size increased from 102 to 152 mm, and relative selectivity peaked at a total length of 638 mm. The estimated lake trout population size-frequency indicated that gillnet catches were negatively biased toward both small and large lake trout. As a consequence of this bias, survival of Lake Superior lake trout across ages 9-11 was underestimated by about 20{\%} when the catch curve was not adjusted for gillnet selectivity.},
author = {Hansen, M J and Madenjian, C P and Selgeby, J H and Helser, T E},
doi = {10.1139/f97-156},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hansen et al/Hansen et al. - 1997 - Gillnet selectivity for lake trout (Salvelinus namaycush) in Lake Superior.pdf:pdf},
isbn = {0706-652X},
issn = {0706-652X},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
keywords = {EXAMPLE,FISHING GEAR,NEBULOSUS,POPULATION,SIZE-SELECTIVITY,SPOTTED SEA-TROUT},
number = {11},
pages = {2483--2490},
title = {{Gillnet selectivity for lake trout (Salvelinus namaycush) in Lake Superior}},
volume = {54},
year = {1997}
}
@article{Cilbiz2015,
author = {Cilbiz, Mehmet and K{\"{u}}{\c{c}}{\"{u}}kkara, Ramazan and Ceylan, Mustafa and Savaşer, Soner and Meke, Turgay},
doi = {10.17216/LimnoFish-5000083989},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Cilbiz et al/Cilbiz et al. - 2015 - Trammel Net Selectivity of Common Carp (Cyprinus carpio L., 1758) in Manyas Lake, Turkey.pdf:pdf},
isbn = {2148-9300},
issn = {2148-9300},
journal = {Journal of Limnology and Freshwater Fisheries Research},
keywords = {cyprinus carpio,select method,selectivity,trammel net},
number = {1},
pages = {1--7},
title = {{Trammel Net Selectivity of Common Carp (Cyprinus carpio L., 1758) in Manyas Lake, Turkey}},
volume = {1},
year = {2015}
}
@misc{Wol1989,
author = {Wolff, M.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Wolff/Wolff - 1989 - A Proposed Method for Standardization of the Selection of Class Intervals for Length Frequency Analysis(2).pdf:pdf},
title = {{A Proposed Method for Standardization of the Selection of Class Intervals for Length Frequency Analysis}},
year = {1989}
}
@article{Science,
author = {Science, Fisheries and Mortality, Management},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Science, Mortality/Science, Mortality - Unknown - Mortality and Survival.pdf:pdf},
pages = {1--9},
title = {{Mortality and Survival.}}
}
@article{Dowling2015,
abstract = {There has been extensive literature discussion regarding data-poor assessments, but considerably less on harvest strategies for data-poor fisheries. There is also a large body of work around harvest strategy development for data-rich fisheries. However, there has been little discussion or specific guidance regarding the process of developing and implementing formal harvest strategies for data-poor fisheries. We outline such a process, illustrated using case studies of data-poor Australian Commonwealth fisheries. The process comprises: (1) compile and review available information; (2) identify possibly indicators; (3) identify reference points for key indicators; (4) select an appropriate harvest strategy and decision rules; (5) if possible, formally evaluate whether the harvest strategy options are likely to achieve the management objectives; and (6) implementation. While this approach is similar to that for data-rich cases, there is less statistical or estimation detail within each step. Even with minimal capacity, the guidelines outlined here, backed by even the simplest form of management strategy evaluation, provide an approach that should enable harvest strategies to be proposed and associated monitoring to be implemented. Monitoring requirements may be explicitly built into harvest strategies via trigger reference points and control rules related to data-collection. While prior formal evaluation provides the best basis for testing the efficacy of a harvest strategy, there remains disparity between the corresponding required capacity and what many agencies and institutions worldwide are capable of providing. Thus, the extent to which harvest strategies may be effectively evaluated and implemented remains an unresolved challenge for data-poor fisheries, but one whose resolution is predicated, at least in the first instance, on adequate monitoring.},
author = {Dowling, N.A. and Dichmont, C.M. and Haddon, M. and Smith, D.C. and Smith, A.D.M. and Sainsbury, K.},
doi = {10.1016/j.fishres.2014.09.013},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Dowling et al/Dowling et al. - 2015 - Guidelines for developing formal harvest strategies for data-poor species and fisheries.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Data-poor assessments,Data-poor fisheries,Data-poor species,Harvest strategy,Management procedure,Management strategy},
pages = {130--140},
publisher = {Elsevier B.V.},
title = {{Guidelines for developing formal harvest strategies for data-poor species and fisheries}},
url = {http://www.sciencedirect.com/science/article/pii/S0165783614002811},
volume = {171},
year = {2015}
}
@article{Erzini1990,
author = {Erzini, Karim},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Erzini/Erzini{\_}1990{\_}SampleSizeandGroupingofDatafor LFA.pdf:pdf},
journal = {Fisheries Research},
pages = {355--366},
title = {{Sample size and grouping of data for length frequency analysis}},
volume = {9},
year = {1990}
}
@article{Dalzell1989,
author = {Dalzell, P and Dalzell, P and Cortez-Zaragoza and Cortez-Zaragoza and Pauly, D. and Pauly, D.},
doi = {10.1111/j.1439-0426.1989.tb00564.x},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Dalzell et al/Dalzell et al. - 1989 - Hook Selectivity of Yellowfin tuna (Thunnus albacares) caught off Darigayos Cove, La Union, Philippines.pdf:pdf},
issn = {0175-8659},
journal = {Journal of Applied Ichthyology},
number = {1},
pages = {12--17},
title = {{Hook Selectivity of Yellowfin tuna (Thunnus albacares) caught off Darigayos Cove, La Union, Philippines}},
volume = {5},
year = {1989}
}
@article{Frusher2003a,
abstract = {From May 1992 to May 1995, tagging of southern rock lobster, Jasus edwardsii, was undertaken in May, February and September in northwestern Tasmania, Australia. Previous modelling of these data using multi-year tagging models produced estimates of annual fishing mortality and tag reporting rates with low relative standard errors and a very low natural mortality estimate (0.0) with high relative standard error. In this model, natural mortality was partitioned within a year by the duration of the time periods and fishing mortality was partitioned by the proportion of fishing effort expended during each period. We altered the model to take advantage of quantitative information on the amount of fishing effort. In the new models, fishing mortality (F) was replaced by catchability (q) multiplied by fishing effort (e) (i.e., F = qe). The most parsimonious model was based on constant catchability over years with unequal catchability among periods within a year. A model with separate catchabilities for each sex did not improve the model. Annual fishing mortality and tag reporting rate estimates had low relative standard errors and were similar to the previous model. The natural mortality estimate (0.12 per year) was higher and more precise than in the previous model and similar to previously published values. Based on Akaike's information criterion (AIC), we found the model based on effort (i.e., F = qe) to be superior to previous models that used effort information merely to apportion fishing mortality to periods of the year. Comparison of the residuals between the two models demonstrated that the inclusion of effort in the model reduced problems with patterns in the residuals. ?? 2003 Elsevier B.V. All rights reserved.},
author = {Frusher, S. D. and Hoenig, J. M.},
doi = {10.1016/j.fishres.2003.09.027},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Frusher, Hoenig/Frusher, Hoenig - 2003 - Recent developments in estimating fishing and natural mortality and tag reporting rate of lobsters using multi-.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Catchability,Fishing and natural mortality,Lobster,Tagging models},
number = {1-3},
pages = {379--390},
title = {{Recent developments in estimating fishing and natural mortality and tag reporting rate of lobsters using multi-year tagging models}},
volume = {65},
year = {2003}
}
@article{Løkkeborg1992,
author = {L{\o}kkeborg, S and Bjordal, {\AA}},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/L{\o}kkeborg, Bjordal/L{\o}kkeborg, Bjordal - 1992 - Species and size selectivity in longline fishing a review.pdf:pdf},
journal = {Fisheries Research},
pages = {311--322},
title = {{Species and size selectivity in longline fishing: a review}},
url = {http://www.sciencedirect.com/science/article/pii/0165783692900847},
volume = {13},
year = {1992}
}
@article{Borgstrom1989,
author = {Borgstr{\"{o}}m, Reidar},
doi = {10.1016/0165-7836(89)90062-3},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Borgstr{\"{o}}m/Borgstr{\"{o}}m - 1989 - Direct estimation of gill-net selectivity for roach (Rutilus rutilus (L.)) in a small lake.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
number = {3},
pages = {289--298},
title = {{Direct estimation of gill-net selectivity for roach (Rutilus rutilus (L.)) in a small lake}},
volume = {7},
year = {1989}
}
@article{William1975,
author = {William, W},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/William/William - 1975 - Least-Squares and Equilibrium Approximation !.pdf:pdf},
number = {1},
title = {{Least-Squares and Equilibrium Approximation !}},
volume = {73},
year = {1975}
}
@book{Pauly1984c,
abstract = {This manual is a selection, from the entire field of fish population dynamics, of methods which are applicable to tropical fish and fisheries and can be implemented with the help of programmable calculators. The methods selected cover the following areas: length-weight relationships, mesh selection, of methods which growth, mortality, population size estimation by various methods (e.g., tagging, virtual population analysis), yield-per-recruit assessments, stock-recruitment relationships, surplu.-yield models, the rate of increase of populations and aspects of multispecies stocks and fisheries. The program. listing and user instructions of thirty programs for use with HP 67/97 programmable calculators are included; the translation of these programs for use with other types of calculators espe- cially HP 41 and TI 59 is discussed. Sixty computational examples including complete keystroke se- quences are provided to illustrate the methods presented in the text. These examples are drawn ex.-iu- sively from subtropical and tropical stocks and fisheries.},
author = {Pauly, D.},
booktitle = {Fisheries Research},
doi = {10.1016/0165-7836(86)90044-5},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly/Pauly - 1984 - Fish population dynamics in tropical waters A manual for use with programmable calculators.pdf:pdf},
isbn = {9711022036},
issn = {01657836},
number = {2},
pages = {171--173},
pmid = {2373},
title = {{Fish population dynamics in tropical waters: A manual for use with programmable calculators}},
volume = {4},
year = {1984}
}
@article{Pet1995,
abstract = {Methods based on the models of Holt (1957) and Sechin (1969a, b) were compared for the estimation of gillnet selectivity for two tilapiine, five cyprinid, two catfish, one goby and one halfbeak species, inhabiting a Sri Lankan reservoir. Holt's model was extended to the case where the standard deviation of the selection curve increases in proportion to the optimum selection length. Sechin's model was extended to the case where standard deviation of body girth increases in proportion to the body girth. Selection curves from extended Holt and Sechin models were compared with length frequency distributions of the catch (catch LFD) for the largest samples per species. A method for rapid estimation of the position and shape of selection curves was proposed. This method is based on the most common position of retention in gillnets, the length-girth relationship at that position and the ratio between mesh perimeter and body girth. A constant coefficient of variation of 9{\%} was considered to be a good estimate for the standard deviation of the selection curves for non-tangled fish. Tangling percentages were low for all but one toothy species, Glossogobius giuris (Hamilton), which showed bimodality in the catch LFD owing to high tangling percentages. The selectivity for different species was compared using the girth at the position of retention as the independent variable. Differences between species were small and a rough estimation for the most efficiently selected retention girth could be calculated as 2.10 times the stretched mesh size, or 1.05 times the mesh perimeter, independent of fish species. The Holt and Sechin models are only suitable to reconstruct population structures of species with low tangling percentages. The extended Holt model is preferred over the Sechin model, because the Sechin model results in selection curves which are systematically more narrow than the catch LFD and Holt selection curves.},
author = {Pet, J. S. and Pet-Soede, C. and {Van Densen}, W. L.},
doi = {10.1016/0165-7836(94)00364-3},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pet, Pet-Soede, Van Densen/Pet, Pet-Soede, Van Densen - 1995 - Comparison of methods for the estimation of gillnet selectivity to tilapia, cyprinids and other fish.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
number = {2},
pages = {141--164},
title = {{Comparison of methods for the estimation of gillnet selectivity to tilapia, cyprinids and other fish species in a Sri Lankan reservoir}},
volume = {24},
year = {1995}
}
@article{Quang2002,
abstract = {The theory of inference of a size distribution for fish captured with size-biased fishing gears is called the “net selectivity problem.” This family of problems arises because of questions about the underlying distribution of the sampled fish, questions about the nature of the size bias, or perhaps questions about the mixtures of species of different sizes. We discuss these problems in the context of size-biased gillnets, although generalization to other kinds of fishing gear is straightforward. We estimate the length distribution of the captured fish, the size distribution of the fish population, and the parameters of the selectivity curves parametrically, using maximum likelihood. To avoid overparametrization we make strong assumptions about the relationship among the selectivity curves, so that fishing power cannot be estimated in this setup. This assumption is called “geometric similarity.” The normal-normal and gamma-gamma combination models are considered, so called because of the shape of the fish-length distribution and the shape of the selectivity curves. The method is demonstrated with a worked simulation example and the American plaice Hippoglossoides platessoides data of Holst and Moth-Poulsen.},
author = {Quang, P X and Geiger, H J C N - AFRB.09.1.016-026},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Quang, Geiger/Quang, Geiger - 2002 - A review of the net selectivity problem and a model for apportioning species based on size-selective sampling.pdf:pdf},
journal = {Alaska Fishery Research Bulletin},
number = {1},
pages = {16--26},
title = {{A review of the net selectivity problem and a model for apportioning species based on size-selective sampling.}},
url = {http://www.adfg.alaska.gov/FedAidpdfs/AFRB.09.1.016-026.pdf},
volume = {9},
year = {2002}
}
@article{Nelson2015,
author = {Nelson, Author Gary A and Nelson, Maintainer Gary A},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Nelson, Nelson/Nelson, Nelson - 2015 - Package ‘ fishmethods '.pdf:pdf},
title = {{Package ‘ fishmethods '}},
year = {2015}
}
@article{Clarke1986,
abstract = {Gillnet selection curves for Atlantic herring (Clupea harengus L.) are calculated using a probability function describing girth retention. The estimated selection curves increased in height and distribution width with increasing mesh size. This is explained by an increase in the difference between maximum girth and gill-girth circumferences as fish size increases. This effect may at least partially explain the empirical results of other workers, and supports the assertion that caution should be observed in applying many of the indirect methods for correcting for gear selection currently in use.},
author = {Clarke, D R and King, P E},
doi = {10.1093/icesjms/43.1.77},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Clarke, King/Clarke, King - 1986 - The estimation of gillnet selection curves for Atlantic herring (Clupea harengus L.) using lengthgirth relations.pdf:pdf},
issn = {1054-3139},
journal = {ICES Journal of Marine Science},
number = {1},
pages = {77--82},
title = {{The estimation of gillnet selection curves for Atlantic herring (Clupea harengus L.) using length/girth relations}},
volume = {43},
year = {1986}
}
@article{Cove1989,
author = {Cove, Darigayos and Union, La},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Cove, Union/Cove, Union - 1989 - f.pdf:pdf},
pages = {12--17},
title = {f},
volume = {1},
year = {1989}
}
@article{Fonteneau2008b,
author = {Fonteneau, A.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Fonteneau/Fonteneau - 2008 - A working proposal for a Yellowfin growth curve to be used during the 2008 yellowfin stock assessment.pdf:pdf},
journal = {Indian Ocean Tuna Commission, IOTC-2008-WPTT-4},
title = {{A working proposal for a Yellowfin growth curve to be used during the 2008 yellowfin stock assessment}},
year = {2008}
}
@article{Sampson2014,
abstract = {Fishery selection (selectivity for short) is the term often used to describe the phenomenon whereby a fish stock experiences mortality due to fishing that is age- or size-specific. Selectivity operates both at a local scale, as in the direct interactions of individual fish with the fishing gear (contact selection), and at a stock-wide scale (population selection), as evidenced by the differential rates of fishing mortality-at-age that are generally observed in stock assessment results. All age-structured stock assessment models have some form of fishery selection to modulate the impact of fishing mortality on differing age-classes, but selection coefficients, from a stock assessment viewpoint, generally are nuisance parameters rather than a focus of attention. This paper provides an overview of the three main processes that contribute to and influence population selection: (1) physical sorting by the fishing gear or differential behavioral responses of the fish to the gear produce the phenomenon of contact selection; (2) differing selection properties of different types of fishing gear (e.g., trawl versus longline) in turn generate a composite selection curve that is a weighted average of the different kinds of contact selection; and (3) when the fish are not well mixed spatially, then the spatial distribution of fishing relative to the spatial distribution of the fish also affects population selectivity. Fishing mortality-at-age estimates derived from a published Virtual Population Analysis of Scotian Shelf haddock are used to illustrate the diversity of shapes that can be seen in population selection curves and their considerable temporal variability. A spatial model for fishery age-selectivity is then used to demonstrate that the maximum relative yield harvested from a stock can be a function of both contact selection and the spatial distribution of fishing.},
author = {Sampson, David B.},
doi = {10.1016/j.fishres.2013.10.004},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Sampson/Sampson - 2014 - Fishery selection and its relevance to stock assessment and fishery management.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Fishery selection curves,Selectivity,Spatial population dynamics},
pages = {5--14},
publisher = {Elsevier B.V.},
title = {{Fishery selection and its relevance to stock assessment and fishery management}},
url = {http://www.sciencedirect.com/science/article/pii/S0165783613002312},
volume = {158},
year = {2014}
}
@article{Jones1984,
author = {Jones, R.},
journal = {FAO Fisheries Technical Paper},
number = {256},
pages = {118p.},
title = {{Assessing the effects of changes in exploitation pattern using length composition data (with notes on VPA and cohort analysis)}},
year = {1984}
}
@article{Jardim2015,
abstract = {There are a large number of commercially exploited stocks lacking quantitative assessments and reliable estimates of stock status. Providing MSY-based advice for these data-limited stocks remains a challenge for fisheries science. For many data-limited stocks, catch length composition and/or survey biomass indices or catch-per-unit effort (cpue) are available. Information on life history traits may also be available or borrowed from similar species/stocks. In this work we present three harvest control rules (HCRs), driven by indicators derived from key monitoring data. These were tested through simulation using two exploitation scenarios (development and over-exploitation) applied to 50 stocks (pelagic, demersal, deep sea species and Nephrops). We examine the performance of the HCRs to deliver catch-based advice that is risk adverse and drives stocks to MSY. The HCR with a biomass index-adjusted status quo catch, used to provide catch-based advice for several European data-limited stocks, showed the poorest performance, keeping the biomass at low or very low levels. The HCRs that adjust the status quo catch based on the variability of the biomass index time series was able to drive most of the stocks to MSY, showing low to moderate biological risk. The recovery of biomass required asymmetric confidence intervals for the biomass index and larger decreases in status quo catch than increases. The HCR based on length reference points as proxies for the F{\textless}inf{\textgreater}SQ{\textless}/inf{\textgreater}/F{\textless}inf{\textgreater}MSY{\textless}/inf{\textgreater} ratio was able to reverse the decreasing trend in biomass but with levels of catch below MSY. This HCR did not prevent some of the stocks declining when subject to over-exploitation. For data-limited stocks, the empirical HCRs tested in this work can provide the basis for catch advice. Nevertheless, applications to real life cases require simulation testing to be carried out to tune the HCRs. Our approach to simulation testing can be used for such analysis.},
author = {Jardim, Ernesto and Azevedo, Manuela and Brites, Nuno M.},
doi = {10.1016/j.fishres.2014.11.013},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Jardim, Azevedo, Brites/Jardim, Azevedo, Brites - 2015 - Harvest control rules for data limited stocks using length-based reference points and survey biomass in.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Data limited stocks,Harvest control rules,Length frequencies,Life History,Risk,Survey indices},
pages = {12--19},
publisher = {Elsevier B.V.},
title = {{Harvest control rules for data limited stocks using length-based reference points and survey biomass indices}},
url = {http://dx.doi.org/10.1016/j.fishres.2014.11.013},
volume = {171},
year = {2015}
}
@article{Finstad2000a,
author = {Finstad, A G and Jansen, P A and Langeland, A},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Finstad, Jansen, Langeland/Finstad, Jansen, Langeland - 2000 - Gillnet selectivity and size and age structure of an alpine Arctic char (Salvelinus alpinus) populai.pdf:pdf},
journal = {Canadian Journal Fisheries Aquatic Science},
keywords = {Arctic char,Norvege,Salvelinus alpinus,age,distribution,filets maillants a maillages multiples,omble chevalier oquassa,taille},
pages = {(p. 1718--1727)},
title = {{Gillnet selectivity and size and age structure of an alpine Arctic char (Salvelinus alpinus) populaion}},
volume = {Vol. 57},
year = {2000}
}
@article{Rivest2015a,
author = {Rivest, Louis-Paul and Baillargeon, Sophie},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Rivest, Baillargeon/Rivest, Baillargeon - 2015 - Package ‘ Rcapture ' from R.pdf:pdf},
pages = {1--57},
title = {{Package ‘ Rcapture ' from R}},
year = {2015}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Froese {\&} Binohlan 2000.doc:doc},
title = {{Froese {\&} Binohlan 2000}}
}
@article{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - MORTALITY.pdf:pdf},
title = {{MORTALITY}}
}
@article{Using,
author = {Using, R},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Using/Using - Unknown - The gillnetfunctions package for R.pdf:pdf},
title = {{The gillnetfunctions package for R}}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Asymptotic Length.Pdf.pdf:pdf},
title = {{Asymptotic Length.Pdf}}
}
@article{Gregoire2003,
author = {Gr{\'{e}}goire, F and Lefebvre, L and Qu{\'{e}}bec, Mont-joli},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gr{\'{e}}goire, Lefebvre, Qu{\'{e}}bec/Gr{\'{e}}goire, Lefebvre, Qu{\'{e}}bec - 2003 - Estimation of gillnet selectivity for Atlantic herring ( Clupea harengus harengus L .) from the we.pdf:pdf},
pages = {1997--2001},
title = {{Estimation of gillnet selectivity for Atlantic herring ( Clupea harengus harengus L .) from the west coast of Newfoundland , 1997-2001 Canadian Industry Report of Fisheries and Aquatic Sciences 272}},
year = {2003}
}
@article{Gislason1985,
abstract = {MSVPAは、自然死亡率をM1とM2に分けたものだ。M2は、捕食者の餌選択、その年間捕食量、平均資源量から計算する。モデルは北海のデータセットでテストした。結果として、捕食は非常に重要であるとわかった。捕食による魚の死亡は、実に漁業による死亡の１．６倍に上った（※ただしこれは合計であることに注意）。さらに、M2の導入は、伝統的なVPAで計算される開発パターンも変えてしまう。},
author = {Gislason, Henrik and Helgason, Th.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gislason, Helgason/Gislason, Helgason - 1985 - Species interaction in assessment of fish stocks with special application to the North Sea.pdf:pdf},
issn = {0106-553X},
journal = {Dana},
number = {1957},
pages = {1--44},
title = {{Species interaction in assessment of fish stocks with special application to the North Sea}},
volume = {5},
year = {1985}
}
@article{Baremore2012a,
abstract = {Gillnet mesh selectivity parameters were estimated for juve- nile blacktip sharks (Carcharhinus limbatus) by using length data from an experimental fishery-independent gillnet survey in the northeastern Gulf of Mexico. Length data for 1720 blacktip sharks were collected over 17 years (1994–2010) with seven mesh sizes ranging from 7.6 to 20.3 cm. Four selectivity models, a normal model assuming f ixed spread, a normal model assuming that spread is proportional to mesh size, a log- normal model, and a gamma model were fitted to the data by using the SELECT (share each length's catch total) method. Each model was run twice under separate assumptions of 1) equal fishing intensity; and 2) fishing intensity proportional to mesh size. The normal, fixed-spread selec- tivity curve where fishing intensity is assumed to be proportional to mesh size provided the best fit to the data according to model deviance estimates and was chosen as the best model. Results indicate that juvenile blacktip sharks are susceptible as bycatch in some commercial gillnet fisheries. Manuscript},
author = {Baremore, Ivy E. and Bethea, Dana M. and Andrews, Kate I.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Baremore, Bethea, Andrews/Baremore, Bethea, Andrews - 2012 - Gillnet selectivity for juvenile blacktip sharks (Carcharhinus limbatus).pdf:pdf},
isbn = {0090-0656},
issn = {00900656},
journal = {Fishery Bulletin},
number = {2},
pages = {230--241},
title = {{Gillnet selectivity for juvenile blacktip sharks (Carcharhinus limbatus)}},
volume = {110},
year = {2012}
}
@article{Powell1979,
author = {Powell, D.G.},
journal = {Rapport Conseil International Exploration de la Mer},
pages = {167--169},
title = {{Estimation of mortality and growth parameters from the length- frequency of a catch}},
volume = {175},
year = {1979}
}
@article{Gheshlaghi2012a,
abstract = {The growth and mortality coefficient of Rutilus frisii kutum, were estimated using length frequency data collected in southern waters of the Caspian Sea during October 2008 to April 2009. The following population parameters were evaluated: length-weight relationship, W = 0.004L 3.258, (r= 0.976); Von Bertalanffy growth constants, W∞ (g) = 4192.3, L∞ (cm) = 70.45, K = 0.2, per year; t0 = −0.75; total mortality and its components, Z = 0.92, M = 0.36, F = 0.56 per year. The exploitation rate (E) was estimated about 0.6. The current yield per- recruit was estimated to be 279.15 g, which was only 1.2{\%} less than Maximum yield per recruitment that was estimated as YPRmax = 287.535, it means if fishing mortality increases from 0.56 per year to 0.7 per year, the yield will raise by only 1.2{\%}. The current YPR and maximum YPR, which were gained at fishing mortality of 0.7, showed that most kutum individuals are caught before reaching the length of maturity. Therefore, to get a maximum YPR, it is necessary to increase fishing effort, even higher than the optimum level. Keeping kutum fishing at the current level will permit harvest of the sustainable yield and avoid overfishing problems.},
author = {Gheshlaghi, P. and Vahabnezhad, A. and {Taghavi Motlagh}, S. A.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gheshlaghi, Vahabnezhad, Taghavi Motlagh/Gheshlaghi, Vahabnezhad, Taghavi Motlagh - 2012 - Growth parameters, mortality rates, yield per recruit, biomass, and MSY of Rutilus fri.pdf:pdf},
issn = {15622916},
journal = {Iranian Journal of Fisheries Sciences},
keywords = {Biomass,Caspian Sea,Exploitation rate,Mortality,Rutilus frisii kutum},
number = {1},
pages = {48--62},
title = {{Growth parameters, mortality rates, yield per recruit, biomass, and MSY of Rutilus frisii kutum, using length frequency analysis in the Southern parts of the Caspian Sea}},
volume = {11},
year = {2012}
}
@article{Clark2014,
abstract = {With large sample sizes, the ratios of the selectivities of two fisheries or surveys at each age or length can be calculated directly (i.e. outside the assessment model) from the age or length compositions of the catches by use of a deterministic equation. These calculated values can serve as a qualitative check on relative selectivity estimates from a model fit. ?? 2013 Elsevier B.V.},
author = {Clark, William G.},
doi = {10.1016/j.fishres.2013.10.017},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Clark/Clark - 2014 - Direct calculation of relative fishery and survey selectivities.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Selectivity,Stock assessment,Survey},
pages = {135--137},
publisher = {Elsevier B.V.},
title = {{Direct calculation of relative fishery and survey selectivities}},
url = {http://dx.doi.org/10.1016/j.fishres.2013.10.017},
volume = {158},
year = {2014}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - vertical histogramms.r:r},
title = {vertical histogramms}
}
@misc{Melville,
author = {Melville, Ruth},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Melville/Melville - Unknown - Literature review.r:r},
issn = {10512276},
pmid = {12136801},
title = {{Literature review.}}
}
@article{Beverton1963,
author = {Beverton, R. J.},
journal = {Rapport Conseil International Exploration de la Mer},
pages = {44--67},
title = {{Maturation, growth and mortality of clupeid and engraulid stocks in relation to fishing}},
volume = {154},
year = {1963}
}
@article{Wolff1989,
author = {Wolff, M},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Wolff/Wolff - 1989 - A proposed method for standardization of the selection of class intervals for length frequency analysis.pdf:pdf},
journal = {Fishbyte},
keywords = {Length frequency theory},
number = {1},
pages = {5},
title = {{A proposed method for standardization of the selection of class intervals for length frequency analysis}},
volume = {7},
year = {1989}
}
@article{Whitney2008,
abstract = {Traditional telemetry methods have been used to quantify the horizontal and vertical displacement of marine species, but are unable to identify specific physical activities such as swimming or gliding, resting, foraging, or spawning. We tested the utility of an acceleration data logger to quantify activity patterns of three captive whitetip reef sharks (Triaenodon obesus) in an enclosed lagoon using internal and external attachment methods. Data obtained using both attachment methods allowed swimming and resting behavior to be differentiated. All sharks showed constant swimming for 514 hours post-tagging before adopting a pattern of daytime rest and nocturnal activity throughout the 616 day deployments. Sharks showed a diel activity pattern, spending 1024{\%} of their time swimming during the day, and 4267{\%} swimming at night. Overall, sharks spent an average of 35 11{\%} (mean SD) of their time swimming. Mean tailbeat frequency was found to be 0.89 0.03 beats s1 in one shark for which it was measured. Respirometry experiments that measured the metabolic rate of two neonate whitetips showed significantly higher metabolic rates at night compared to the day. When taken in conjunction with the acceleration data, these results suggest that whitetips are nocturnally active and show diel circadian rhythms shortly after birth. Our study demonstrates that acceleration data loggers can be used to quantify activity patterns and offer promise for quantifying energy budgets of various reef sharks both in captivity and in the field.},
author = {Whitney, Nicholas M and Papastamatiou, Yannis P and Holland, Kim N and Lowe, Christopher G},
doi = {10.1051/alr},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Whitney et al/Whitney et al. - 2008 - Use of an acceleration data logger to measure diel activity patterns in captive whitetip reef sharks , Triaenodo.pdf:pdf},
isbn = {0990-7440},
issn = {09907440},
journal = {Aquatic Living Resources},
keywords = {accelerometer,diel cycles,elasmobranch,respirometry},
number = {2007},
pages = {299--305},
title = {{Use of an acceleration data logger to measure diel activity patterns in captive whitetip reef sharks , Triaenodon obesus}},
url = {http://www.alr-journal.org/articles/alr/abs/2007/04/alr041-07/alr041-07.html},
volume = {20},
year = {2008}
}
@article{Chen1997a,
abstract = {Yield-per-recruit models are of'ten used to provide management guidance for the efficient use of a fish cohort and to cstimate the biological reference points, such as F,,, or FM,,. Although model parameters are usually age-specific, these parameters are thought to he more likely related to length than age. In this study, age- and length-structured models are compared in calculating yield per recruit, I.;,,,a, nd FMAXa t which the yield per recruit is maximized. Using a Monte Carlo simulation approach, 1 also compare differences in effects of uncertainties of' the model parameters on yield-per-rccruit analysis and estimation of F,, and t.,,, using agc- and Icngth-structured models. This study shows that differences are small in estimating yield per recruit, F,,,. and FMAX using two types of models when there are no error variances in the model parameters. However, such differences increase with the uncertainties of the model paramctcrs. The yieldper recruit, t.;, ,, and FMax estimated using the age-structurcd model tend to have smaller values and variations compared with those estimated using the length-structured model. This study indicates that although the length-structurcd model can better incorporate the information observed from fisheries, age-structured yield-pcr-rccruit modcl can provide estimates of yield per recruit, F,,,, and FM,, more precisely and more conservatively, and thus is preferred from the conservation viewpoint in fisheries management.},
author = {Chen, Yong},
doi = {10.1051/alr:1997030},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Chen/Chen - 1997 - A cornparison study of age- and length-structured yield-per-recruit models.pdf:pdf},
isbn = {0990-7440},
issn = {0990-7440},
journal = {Aquatic Living Resources},
keywords = {Fishery management,mathematical models,stock asscssment.,yield},
pages = {271--280},
title = {{A cornparison study of age- and length-structured yield-per-recruit models}},
volume = {10},
year = {1997}
}
@article{Pauly2013,
author = {Pauly, D. and Greenberg, A.},
journal = {Fisheries Centre Research Reports},
pages = {52},
title = {{ELEFAN in R: a new tool for length-frequency analysis}},
volume = {21},
year = {2013}
}
@article{Package2014,
author = {Package, Type and Gerritsen, Author Hans},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Package, Gerritsen/Package, Gerritsen - 2014 - Package ‘ mapplots '.pdf:pdf},
title = {{Package ‘ mapplots '}},
year = {2014}
}
@article{Prager1996,
abstract = {Should a surplus production model be applied to a stock that exhibits pronounced age structure? Should it be applied to a stock that has experienced changing fishing mortality rates on fish of different sizes over time (i.e., changing selectivity)? These questions are of general interest to those engaged in stock assessment and of particular interest in the assessment of North Atlantic swordfish Xiphias gladius. In an attempt to answer them, we simulated an age-structured population, with fishery, similar to that of swordfish in the North Atlantic. The 30-year simulation included biological characteristics from the literature on swordfish and simulated fishing with increasing mortality of young fish over time; simulated catches approximated the actual catches of swordfish from 1962 through 1991. We fit a lumped-biomass, dynamic surplus production model to summary non-age-structured data from the simulated fishery. The resulting parameter estimates were compared to management benchmarks, including maximum sustainable yield (MSY), computed by age-structured methods from the growth and recruitment characteristics of the underlying simulation. The changing selectivity resulted in a small ({\textless}10{\%}) decrease in MSY from the beginning of the series to its end; estimates from the production model were close to these underlying MSY values. Nine additional population trajectories were simulated with the same biological characteristics but other fishing histories; in most cases, the production model provided qualitatively correct estimates of stock status. Two new reliability statistics appear to be of value in judging the quality of production model fits. We conclude that for stocks similar to swordfish, the presence of strong age structure and moderate changes in selectivity should not proscribe the application of simple production models.},
author = {Prager, Michael H. and Goodyear, C. Phillip and Scott, Gerald P.},
doi = {10.1577/1548-8659(1996)125<0729:AOASPM>2.3.CO;2},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prager, Goodyear, Scott/Prager, Goodyear, Scott - 1996 - Application of a Surplus Production Model to a Swordfish-Like Simulated Stock with Time-Changing Gear S.pdf:pdf},
isbn = {0002-8487},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
number = {Goodyear},
pages = {729--740},
title = {{Application of a Surplus Production Model to a Swordfish-Like Simulated Stock with Time-Changing Gear Selectivity}},
volume = {125},
year = {1996}
}
@article{Pauly1981a,
abstract = {computer based method for tracing growth curves through fish length frequency samples sequentially arranged in time. },
author = {Pauly, D and David, N},
doi = {10.1007/BF01500694},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly, David/Pauly, David - 1981 - ELEFAN I, a BASIC program for the objective extraction of growth parameters from length-frequency data.pdf:pdf},
journal = {ICLARM contribution},
number = {32},
pages = {205--211},
pmid = {775},
title = {{ELEFAN I, a BASIC program for the objective extraction of growth parameters from length-frequency data}},
volume = {32},
year = {1981}
}
@article{Millar2016,
author = {Millar, Colin P. and Fryer, Robert J. and Millidine, Karen J. and Malcolm, Iain A.},
doi = {10.1016/j.fishres.2016.01.001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Millar et al/Millar et al. - 2016 - Modelling capture probability of Atlantic salmon (Salmo salar) from a diverse national electrofishing dataset Imp.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
number = {January},
pages = {1--12},
title = {{Modelling capture probability of Atlantic salmon (Salmo salar) from a diverse national electrofishing dataset: Implications for the estimation of abundance}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783616300017},
volume = {177},
year = {2016}
}
@article{Bentley2015,
author = {Bentley, Nokome},
doi = {10.1093/icesjms/fsu023},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Bentley/Bentley - 2014 - Approaches and Solutions.pdf:pdf},
journal = {ICES Journal of Marine Science},
keywords = {data-poor,estimation,stock assessment},
number = {1},
pages = {186--193},
title = {{Data and time poverty in fisheries estimation: potetnial approaches and solutions}},
volume = {72},
year = {2015}
}
@article{Soriano1986a,
author = {Soriano, Mina L},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Soriano/Soriano - 1986 - Some Practical Extensions to Beverton and Holt ' s Relative Yield-Per-Recruit Model.pdf:pdf},
journal = {Fisheries (Bethesda)},
number = {Jones 1957},
pages = {491--495},
title = {{Some Practical Extensions to Beverton and Holt ' s Relative Yield-Per-Recruit Model *}},
year = {1986}
}
@article{Haimovici2007,
abstract = {Longlines lose fishing power with soaking time due to bait losses and hooked fishes. Because logbook records and dockside interviews usually do not include detailed data on fishing power loss, relative densities in commercial fishing are estimated as the number or weight of fishes caught per hook and unit of time. To investigate the influence of the fishing power loss of bottom longlines on relative density estimates, data of 188 standardized hauls of 1000 hooks, baited with squid and soaked for 3 h in average were analyzed. The estimates given by the number of fish caught per 1000-hook-hour (CPUE) were compared to those from the partial removal instantaneous rates (??) caused by each species, an index that requires detailed information that takes into account the progressive decrease in the number of baited hooks available to fish. It was found that, for relatively short hauls observed in commercial fishing operations in Southern Brazil, the patterns of bathymetric and latitudinal distribution of the three most numerous species in the catch did not differ significantly when calculated in either units. Nevertheless, high initial catch rates resulted in lower correlation between both measures. It was concluded that the analysis of CPUE from bottom longline commercial fishing catches can result in reliable information on the distribution and relative abundance of the target species in the fishery. ?? 2007 Elsevier B.V. All rights reserved.},
author = {Haimovici, Manuel and ??vila-da-Silva, Ant??nio Olinto},
doi = {10.1016/j.fishres.2007.01.003},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Haimovici, vila-da-Silva/Haimovici, vila-da-Silva - 2007 - A comparison of methods for estimating relative abundances in bottom longline fishery surveys.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Catch and effort,Demersal fishes,Fishing power,Longline},
number = {1-2},
pages = {226--231},
title = {{A comparison of methods for estimating relative abundances in bottom longline fishery surveys}},
volume = {85},
year = {2007}
}
@article{Fox1971,
author = {Fox, Ww},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Fox/Fox - 1971 - Random variability and parameter estimation for the generalized production model.pdf:pdf},
journal = {Fishery Bulletin},
number = {3},
pages = {569--580},
title = {{Random variability and parameter estimation for the generalized production model}},
url = {http://fishbull.noaa.gov/69-3/fox.pdf},
volume = {69},
year = {1971}
}
@article{Hart2009,
author = {Hart, Deborah R and Chute, Antonie S},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hart, Chute/Hart, Chute - 2009 - Estimating von Bertalanffy growth parameters from growth increment data using a linear mixed-effects model , with a.pdf:pdf},
keywords = {166 water st,2369,2393,accepted 4 june 2009,advance access publication 8,chute,correspondence to d,d,deborah,e-mail,fax,gov,hart,hart and a,july 2009,ma 02543,marine protected areas,mixed-effects model,noaa,northeast fisheries science center,placopecten magellanicus,r,received 13 november 2008,s,scallop,tel,usa,von bertalanffy growth,woods hole,þ 1 508 495},
number = {Figure 1},
title = {{Estimating von Bertalanffy growth parameters from growth increment data using a linear mixed-effects model , with an application to the sea scallop Placopecten magellanicus}},
year = {2009}
}
@article{Andrew2007,
abstract = {Small-scale fisheries (SSF) make important but undervalued contributions to the; ; economies of some of the world's poorest countries. They also provide much of the; ; animal protein needed by societies in which food security remains a pressing issue.; ; Assessment and management of these fisheries is usually inadequate or absent and; ; they continue to fall short of their potential as engines for development and social; ; change. In this study, we bring together existing theory and methods to suggest a; ; general scheme for diagnosing and managing SSF. This approach can be adapted to; ; accommodate the diversity of these fisheries in the developing world. Many threats; ; and solutions to the problems that beset SSF come from outside the domain of the; ; fishery. Significant improvements in prospects for fisheries will require major changes; ; in societal priorities and values, with consequent improvements in policy and; ; governance. Changes in development policy and science reflect these imperatives but; ; there remains a need for intra-sectoral management that builds resilience and; ; reduces vulnerability to those forces beyond the influence of small-scale fishers.},
author = {Andrew, Neil and B{\'{e}}n{\'{e}}, Christophe and Hall, Stephen J and Allison, Edward H and Heck, Simon and Ratner, Blake D},
doi = {10.1111/j.1467-2679.2007.00252.x},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Andrew et al/Andrew et al. - 2007 - Diagnosis and management of small-scale fisheries in developing countries.pdf:pdf},
isbn = {1467-2979},
issn = {1467-2960},
journal = {Fish And Fisheries},
keywords = {development,management,poverty,resilience,small-scale fisheries},
number = {227},
pages = {227--240},
pmid = {285},
title = {{Diagnosis and management of small-scale fisheries in developing countries}},
volume = {8},
year = {2007}
}
@article{Bhattacharya2016,
author = {Bhattacharya, Author C G},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Bhattacharya/Bhattacharya - 2016 - A Simple Method of Resolution of a Distribution into Gaussian Components Published by International Biometric Soc.pdf:pdf},
number = {1},
pages = {115--135},
title = {{A Simple Method of Resolution of a Distribution into Gaussian Components Published by : International Biometric Society Stable URL : http://www.jstor.org/stable/2528285 REFERENCES Linked references are available on JSTOR for this article : You may need to}},
volume = {23},
year = {2016}
}
@incollection{Tukey1986,
address = {Monterey, CA, USA},
author = {Tukey, J},
booktitle = {The Collected Works of John W. Tukey- philosophy and principles of data analysis: 1965-1986 (Vol. 4, pp. 517-549).},
editor = {Jones, L. V.},
publisher = {Wadsworth {\&} Brooks/Cole},
title = {{The future of processes of data analysis}},
year = {1986}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - 20005b75{\_}293.pdf.pdf:pdf},
title = {20005b75{\_}293.pdf}
}
@article{Fulton2004a,
abstract = {The Integrated Generic Bay Ecosystem Model (IGBEM) is presented. It is a coupled physical transport-biogeochemical process model constructed as a basis to explore the effects of model structure and complexity. The foundations for the model are two existing models, the European Regional Seas Ecosystem Model II (ERSEM II) and the Port Phillip Bay Integrated Model (PPBIM). Additional functional groups (such as benthic herbivorous invertebrates) and modules (dealing with sediment chemistry and mixing) have been incorporated or modified to ensure a more complete representation of temperate bay ecosystems and their processes, and a seamless amalgam of ERSEM II and PPBIM. The standard form of the entire model compares well with real ecosystems, such as Port Phillip Bay in Australia, and conforms to general ecological checkpoints such as the expected Sheldon Spectrum and Monbet's relationship between chlorophyll a and dissolved inorganic nitrogen. The model also produces spatial zonation and long-term cycles characteristic of natural systems. Despite the model taking a generalised biomass per functional group form, it captures well the system dynamics and allows for exploration of the effects of ecological driving forces such as predation and competition. {\textcopyright} 2003 Elsevier B.V. All rights reserved.},
author = {Fulton, Elizabeth A. and Smith, Anthony D M and Johnson, Craig R.},
doi = {10.1016/j.ecolmodel.2003.09.027},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Fulton, Smith, Johnson/Fulton, Smith, Johnson - 2004 - Biogeochemical marine ecosystem models I IGBEM - A model of marine bay ecosystems.pdf:pdf},
isbn = {0304-3800},
issn = {03043800},
journal = {Ecological Modelling},
keywords = {Biogeochemical model,Ecosystem dynamics,Ecosystem processes},
number = {3},
pages = {267--307},
title = {{Biogeochemical marine ecosystem models I: IGBEM - A model of marine bay ecosystems}},
volume = {174},
year = {2004}
}
@article{Die1997,
author = {Die, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Die/Die - 1997 - Biomass Dynamic Models.pdf:pdf},
pages = {1997},
title = {{Biomass Dynamic Models}},
year = {1997}
}
@article{Punt1997,
abstract = {The Bayesian approach to stock assessment determines the probabilities of alternative hypotheses using information for the stock in question and from inferences for other stocks/species. These probabilities are essential if the consequences of alternative management actions are to be evaluated through a decision analysis. Using the Bayesian approach to stock assessment and decision analysis it becomes possible to admit the full range of uncertainty and use the collective historical experience of fisheries science when estimating the consequences of proposed management actions. Recent advances in computing algorithms and power have allowed methods based on the Bayesian approach to be used even for fairly complex stock assessment models and to be within the reach of most stock assessment scientists. However, to avoid coming to ill-founded conclusions, care must be taken when selecting prior distributions. In particular, selection of priors designed to be noninformative with respect to quantities of interest to management is problematic. The arguments of the paper are illustrated using New Zealand's western stock of hoki, Macruronus novaezelandiae (Merlucciidae) and the Bering–Chukchi– Beaufort Seas stock of bowhead whales as examples.},
author = {Punt, a E and Hilborn, R},
doi = {10.1023/A:1018419207494},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Punt, Hilborn/Punt, Hilborn - 1997 - Fisheries stock assessment and decision analysis the Bayesian approach.pdf:pdf},
isbn = {0960-3166},
issn = {0960-3166, 1573-5184},
journal = {Reviews in Fish Biology and Fisheries},
number = {1},
pages = {35--63},
title = {{Fisheries stock assessment and decision analysis: the Bayesian approach}},
volume = {7},
year = {1997}
}
@article{Foster2015,
author = {Foster, Author Scott D and Foster, Maintainer Scott},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Foster, Foster/Foster, Foster - 2015 - Package ‘ fishMod '.pdf:pdf},
title = {{Package ‘ fishMod '}},
year = {2015}
}
@article{Powers2014,
author = {Powers, J. E.},
journal = {ICES Journal of Marine Science: Journal du Conseil},
number = {7},
pages = {1629--1637},
title = {{Age-specific natural mortality rates in stock assessments: size-based vs. density-dependent}},
volume = {71},
year = {2014}
}
@article{Beverton1956,
author = {Beverton, R. J. H. and Holt, S. J.},
journal = {Rapport Conseil International Exploration de la Mer},
number = {1},
pages = {67--83},
title = {{A review of methods for estimating mortality rates in exploited fish populations, with special reference to sources of bias in catch sampling}},
volume = {140},
year = {1956}
}
@article{Prager2013,
author = {Prager, Michael H and Consulting, Prager},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prager, Consulting/Prager, Consulting - 2013 - User ' s Guide for ASPIC A Stock – Production Model.pdf:pdf},
title = {{User ' s Guide for ASPIC : A Stock – Production Model ; ; ;}},
year = {2013}
}
@article{Russo2014,
abstract = {VMSbase is an R package devised to manage, process and visualize information about fishing vessels activity (provided by the vessel monitoring system--VMS) and catches/landings (as reported in the logbooks). VMSbase is primarily conceived to be user-friendly; to this end, a suite of state-of-the-art analyses is accessible via a graphical interface. In addition, the package uses a database platform allowing large datasets to be stored, managed and processed vey efficiently. Methodologies include data cleaning, that is removal of redundant or evidently erroneous records, and data enhancing, that is interpolation and merging with external data sources. In particular, VMSbase is able to estimate sea bottom depth for single VMS pings using an on-line connection to the National Oceanic and Atmospheric Administration (NOAA) database. It also allows VMS pings to be assigned to whatever geographic partitioning has been selected by users. Standard analyses comprise: 1) m{\'{e}}tier identification (using a modified CLARA clustering approach on Logbook data or Artificial Neural Networks on VMS data); 2) linkage between VMS and Logbook records, with the former organized into fishing trips; 3) discrimination between steaming and fishing points; 4) computation of spatial effort with respect to user-selected grids; 5) calculation of standard fishing effort indicators within Data Collection Framework; 6) a variety of mapping tools, including an interface for Google viewer; 7) estimation of trawled area. Here we report a sample workflow for the accessory sample datasets (available with the package) in order to explore the potentialities of VMSbase. In addition, the results of some performance tests on two large datasets (1×10(5) and 1×10(6) VMS signals, respectively) are reported to inform about the time required for the analyses. The results, although merely illustrative, indicate that VMSbase can represent a step forward in extracting and enhancing information from VMS/logbook data for fisheries studies.},
author = {Russo, Tommaso and D'Andrea, Lorenzo and Parisi, Antonio and Cataudella, Stefano},
doi = {10.1371/journal.pone.0100195},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Russo et al/Russo et al. - 2014 - VMSbase An R-Package for VMS and logbook data management and analysis in fisheries ecology.pdf:pdf},
issn = {19326203},
journal = {PLoS ONE},
number = {6},
pmid = {24932915},
title = {{VMSbase: An R-Package for VMS and logbook data management and analysis in fisheries ecology}},
volume = {9},
year = {2014}
}
@article{Dharmendra2005,
author = {Dharmendra, Degambur and S{\'{o}}lmundsson, J{\'{o}}n},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Dharmendra, S{\'{o}}lmundsson/Dharmendra, S{\'{o}}lmundsson - 2005 - Stock assessment of the offshore Mauritian banks using dynamic biomass models and analysis of lengt(2).pdf:pdf},
journal = {Fisheries Training Program The United Nations University},
keywords = {banks fishery,bootstrap,dynamic biomass models,f msy,hind-casting trials,lethrinus mahsena,malha,mauritius,msy,nazareth,saya de,tac,unu-fisheries training programme},
pages = {61},
title = {{Stock assessment of the offshore Mauritian banks using dynamic biomass models and analysis of length frequency of the Sky emperor (Lethrinus mahsena)}},
year = {2005}
}
@book{Beverton1957,
abstract = {This volume, in 4 parts, contains the theoretical development of simple and complex deterministic models, and their application to 2 North Sea fisheries. Four primary factors which change the total weight of the fishable stock, recruitment, growth, capture, and "natural" death, are considered. I. The development of a theory of fishing, each factor represented by constant and independent parameters. The 4 primary factors are brought together by considering a year-class of recruits to the fished area, and by applying the other 3 factors to deduce the total yield of the year-class throughout its life, equivalent to the steady state yield in 1 year from all year-classes. From this equation are derived expressions for yield in number, catch per unit of effort, population number, population biomass, and mean length, weight and age of fish in the population and in the catch. II. The theory is extended to include the effects of change in, and interaction between, primary factors. Recruitment is usually but not always independent of population density in marine fishes. A relationship between egg-production (E) and recruitment (R) is developed, in which R approaches an asymptote as E increases indefinitely, with E proportional to adult stock weight and prerecruit mortality rates a linear function of the density of young fish. Since E is related to biomass, fecundity and pre-recruitment mortality can be substituted for the recruitment terms in the yield equation. To test whether a regulated fishery is behaving as expected, a model is derived relating variations in R and annual yield. Other possible types of relationship between R and E are considered more briefly. Capture and natural death: Variations with age in both natural (M) and fishing (F) mortality are considered; M in relation to stock density, F to mesh selection and ability to avoid the net. Methods are developed for dealing with seasonal variation in fishing intensity and with "transitional" periods between periods of steady state. The lack of uniformity in the spatial distribution of fish and fishing effort, involving an analysis of the movements within the exploited area is investigated. Growth: Even though growth is variable, von Bertalanffy's equation remains the most suitable formulation. Methods are discussed Df considering variations in growth with age, between individual fish, and due to dependence on food consumption. The latter is treated mainly by an analysis of the interaction between the fish population and its food supply, including the dynamics of the latter. Equations are derived for actual and maximal food consumption of a fish population in terms of its abundance, age-composition, and growth rate. Consideration of the effects introduced by predation on 2 or more food species lead to a review of methods of reporting food preference and vulnerability. Methods developed for populations of single species are extended to fisheries based on several species caught together by the same gear. III. Estimation of parameters for North Sea plaice and haddock stocks. A basic unit of standardized fishing effort of a steam trawler ton-hour is suggested, and the same per square mile as an index of density. Estimates of the total fishing mortality coefficient (F+M), made from catch per unit of effort and age-composition data were 0.83 for plaice and 1.2 for haddock during the inter-war period. Methods of obtaining separate estimates of F and M from marking experiments are discussed; 2 earlier methods are found to be erroneous and a simple method of estimating F, clear of rate of shedding of marks and other errors is given. An average value of F of 1.5 for plaice was obtained for the most heavily fished portions of the southern North Sea during the post-war period. The magnitudes of dispersion to other areas, and of shedding rates prevented any estimate of M. In considering the variation in F with age as a result of mesh selection, a close proportional relation between the 50{\%} selection point and mesh size was found, the factor being 2.2 for plaice and 3.3 for haddock. Separate estimates of F and M from age-composition and effort data were not possible. However, data on the abundance of certain year-classes sampled both in 1938-39 and 1945-46 yielded an estimate of M of 0.1 for plaice in the prewar period. F was thus 0.73. Although no accurate estimate of M for haddock is available, certain age-composition data suggest it is not much greater than 0.2. F for the pre-war period was thus 1.0. In North Sea plaice, recruitment (R) occurs by an off-shore movement, following the law of random diffusion at a rate of about 1 mile a day. About 90{\%} of the recruits are in age-groups IE and IV, the average age being 3.7 years. In the earlier war period average R was 250 million plaice and 850 million haddock. The fishable stock of plaice averaged 350 million. While there is some indication of a relation between egg-production and recruitment in haddock, in plaice results are inconclusive. A review of this relationship in certain other species is also given. In growth equations, the simple cube length-weight relationship appears in plaice and haddock; an allometric expression is not recommended. Von Bertalanffy's equation is fitted to data for plaice, haddock, cod and sole. In plaice and haddock, an empirical relation between growth and population density is found, derived from data referring in the former to steady states, in the latter to annual fluctuations. The dependence of growth on feeding and food supply is examined in plaice only. Maintenance food requirements are almost exactly proportional to the two-thirds power of body weight; the efficiency of utilization 9f Mytilus flesh for growth is about 0.2. An analysis of the variation of utilization efficiency with amount of food eaten showed that the limiting growth parameter (Wimage l) is in order of magnitude some 5 or 6 times Wimage for North Sea plaice. IV. The properties of various theoretical models and conclusions drawn therefrom. The simple models show that a greater steady state yield of plaice and haddock than in the prewar period could be obtained with either a lower fishing intensity (affecting F) or a larger mesh size (affecting the age, tpimage at which the fish enter the exploited phase). An even greater yield would result by adjustment of both F and tpimage than by either alone. Variation of population biomass, numbers, average size and age of fish in the catch with F and tpimage are examined. Relatively small differences in plaice yield occur with changes in maximum age, except at low values of F, and with M within 50{\%} of its estimated value (0.1). In the more complex models, the more exact representation of some properties, e.g. mesh selection and recruitment, produce little difference in the yield curves when compared to simpler approximations. Variation with population density can cause important differences. When M increases linearily with density, yield curves have lower maxima, located closer to prewar values of F and iff than with M constant. When the dynamics of food populations are introduced, yield curves resemble those obtained with a linear relationship, thus indicating that the latter is likely to give reasonably satisfactory assessments of the effects of density dependent growth. Where recruitment depends on stock size, both recruitment and growth should be simultaneously density dependent. Changes in recruitment can then still outweigh those in growth, causing yield curves to have higher maxima than if all factors were density independent. Yield curves are little affected if fishing is restricted to not less than three-quarters of the stock area. With further reductions, the maxima become less marked and occur at higher values of F as in a coastal fishery where the main bulk of the population is unfished but acts as a reserve. In general, when complex changes in the primary factors are considered, the actual changes in fishing intensity and especially in mesh size required to produce a larger steady yield are not as great as would be predicted from simple models. In a discussion of the general principles and methods of fishery regulation, the concept is developed of eumetric fishing - the achievment, by adjustment of gear selectivity, of the greatest yield possible with any particular amount of fishing. Yield increases with increasing fishing intensity but at a decreasing rate and without passing through a maximum. When these assumptions apply, the conventional idea of adjusting the amount of fishing to obtain the maximum steady state yield must be abandoned. The decision as to which point on a eumetric yield curve a fishery is to operate is economic and social, depending on how much of the maximum potential profit is to be realized as such and how the remainder is to be absorbed. To obtain the benefits of gear selectivity some control of fishing power is essential. The greatest yield of demersal fish from the North Sea, compatible with avoiding any serious loss of sole or whiting, would be obtained with a fishing effort not more than half, and perhaps less, of the pre-war effort, and a mesh size of 80 to 90 mm. The increase in yield could be 25 to 50{\%}. The proposals of the 1946 Overfishing Conference to reduce overall fishing effort to 85{\%} of the pre-war level and to increase mesh size to 80 mm may result in an increase of 6 to 10{\%} in the total landings of the 4 major North Sea trawl fisheries. ABSTRACT AUTHORS: F. H. C. Taylor},
author = {Beverton, Raymond J H and Holt, Sidney J},
booktitle = {Fisheries Investigations Series 2: Sea Fisheries},
doi = {10.1007/BF00044132},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Beverton, Holt/Beverton, Holt - 1957 - On the Dynamics of Exploited Fish Populations.pdf:pdf},
isbn = {0960-3166},
issn = {0960-3166},
number = {2},
pages = {540},
pmid = {21727890},
title = {{On the Dynamics of Exploited Fish Populations}},
url = {https://books.google.com/books?hl=en{\&}lr={\&}id=BqbnCAAAQBAJ{\&}pgis=1},
volume = {4},
year = {1957}
}
@article{Porch2002,
author = {Porch, Clay E and Fisher, Mark R and Mceachron, Lawrence W},
doi = {10.1139/F02-034},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Porch, Fisher, Mceachron/Porch, Fisher, Mceachron - 2002 - Estimating abundance from gillnet samples with application to red drum ( Sciaenops ocellatus ) in Texa.pdf:pdf},
isbn = {1205-7533},
issn = {12057533},
journal = {Fisheries (Bethesda)},
pages = {657--668},
title = {{Estimating abundance from gillnet samples with application to red drum ( Sciaenops ocellatus ) in Texas bays}},
volume = {668},
year = {2002}
}
@misc{Schaefer1957,
author = {Schaefer, Milner B.},
booktitle = {Bulletin of the Inter-American Tropical Tuna Commission},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Schaefer/Schaefer - 1957 - A study of the dynamics of the fishery for yellowfin tuna in the eastern tropical pacific ocean.pdf:pdf},
number = {6},
pages = {247--284},
title = {{A study of the dynamics of the fishery for yellowfin tuna in the eastern tropical pacific ocean}},
volume = {11},
year = {1957}
}
@book{Macdonald1988,
author = {Macdonald, P.D.M. and Green, P.E.J.},
booktitle = {Ichthus Data Systems},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Macdonald, Green/Macdonald, Green - 1988 - User's guide ti program MIX an interactive program for fitting mixtures of distributions.pdf:pdf},
isbn = {0969230516},
number = {January},
pages = {1--59},
title = {{User's guide ti program MIX: an interactive program for fitting mixtures of distributions}},
year = {1988}
}
@article{Hewitt2007,
abstract = {Analyses of the population dynamics of blue crab have been complicated by a lack of estimates of the instantaneous natural mortality rate (M). We developed the first direct estimates of M for this species by solving Baranov's catch equation for M given estimates of annual survival rate and exploitation rate. Annual survival rates were estimated from a tagging study on adult female blue crabs in Chesapeake Bay, and female-specific exploitation rates for the same stock were estimated by comparing commercial catches with abundances estimated from a dredge survey. We also used eight published methods based on life history parameters to calculate indirect estimates of M for blue crab. Direct estimates of M for adult females in Chesapeake Bay for the years 20022004 ranged from 0.42 to 0.87 per year and averaged 0.71 per year. Indirect estimates of M varied considerably depending on life history parameter inputs and the method used. All eight methods yielded values for M between 0.99 and 1.08 per year, and six of the eight methods yielded values between 0.82 and 1.35 per year. Our results indicate that natural mortality of blue crab is higher than previously believed, and we consider M values between 0.7 and 1.1 per year to be reasonable for the exploitable stock in Chesapeake Bay. Remaining uncertainty about M makes it necessary to evaluate a range of estimates in assessment models.},
author = {Hewitt, David a. and Lambert, Debra M. and Hoenig, John M. and Lipcius, Romuald N. and Bunnell, David B. and Miller, Thomas J.},
doi = {10.1577/T06-078.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hewitt et al/Hewitt et al. - 2007 - Direct and Indirect Estimates of Natural Mortality for Chesapeake Bay Blue Crab.pdf:pdf},
isbn = {0002-8487},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
number = {4},
pages = {1030--1040},
title = {{Direct and Indirect Estimates of Natural Mortality for Chesapeake Bay Blue Crab}},
volume = {136},
year = {2007}
}
@article{Centre2013,
author = {Centre, Fisheries},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Centre/Centre - 2013 - Fisheries Centre Research Reports ELEFAN in R A new tool for length-frequency analysis.pdf:pdf},
title = {{Fisheries Centre Research Reports ELEFAN in R : A new tool for length-frequency analysis}},
year = {2013}
}
@article{Record2014,
author = {Record, Nicholas R and Pershing, Andrew J and Cropp, Roger and Norbury, John and Record, Nicholas R and Pershing, Andrew J},
doi = {10.1093/icesjms/fst176},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Record et al/Record et al. - 2014 - Marine Science.pdf:pdf},
isbn = {2068603217},
issn = {1206616369},
journal = {ICES Journal of Marine Science},
keywords = {1961,biodiversity,coexistence,competitive exclusion,ecosystem modelling,focus on the maintenance,has compelled ecologists to,hereafter,hutchinson,linear mortality,npz,of coexistence of competing,paradox i,paradox of the plankton,plankton,species in ecological models,the,these},
pages = {236--240},
title = {{Marine Science}},
volume = {71},
year = {2014}
}
@article{Ennis1997,
abstract = {H2 reduction of Aromatic amino acids},
author = {Ennis, B.J. and Litster, J.D.},
doi = {10.1081/E-EEE2-120046011},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Ennis, Litster/Ennis, Litster - 1997 - {\textcopyright} Respect Copyright {\textcopyright} Encourage Creativity {\textcopyright}.pdf:pdf},
isbn = {9783937655239},
issn = {00976156},
journal = {Knowledge Creation Diffusion Utilization},
pages = {20--54},
title = {{{\textcopyright} Respect Copyright {\textcopyright} Encourage Creativity {\textcopyright}}},
year = {1997}
}
@book{Pauly1987a,
author = {Pauly, D and Morgan, GR},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly, Morgan/Pauly, Morgan - 1987 - Length-based methods in fisheries research(2).pdf:pdf},
isbn = {9711022281},
title = {{Length-based methods in fisheries research}},
url = {http://books.google.com/books?hl=en{\&}lr={\&}id=R4DC-ALyducC{\&}oi=fnd{\&}pg=PR7{\&}dq=Length-Based+Methods+in+Fisheries+Research{\&}ots=ui8PSeeg51{\&}sig=4ncDFoq-WN5Vej56XIZ5y2oeB50},
year = {1987}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - FishTropR{\_}literature{\_}review.rtf:rtf},
title = {{FishTropR{\_}literature{\_}review}}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Moreau and Maraite 1999.Pdf.pdf:pdf},
title = {{Moreau and Maraite 1999.Pdf}}
}
@article{Grundlagen,
author = {Grundlagen, I},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Grundlagen/Grundlagen - Unknown - Zur Mathematik des tierischen Wachstums.pdf:pdf},
title = {{Zur Mathematik des tierischen Wachstums}}
}
@article{Wickham2011a,
abstract = {Software testing is important, but many of us don't do it because it is frustrating and boring. testthat is a new testing framework for R that is easy learn and use, and integrates with your existing workflow. This paper shows how, with illustrations from existing packages.},
author = {Wickham, Hadley},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Wickham/Wickham - 2011 - testthat Get Started with Testing.pdf:pdf},
issn = {2073-4859},
journal = {The R Journal},
number = {June},
pages = {5--10},
title = {{testthat: Get Started with Testing}},
volume = {3},
year = {2011}
}
@article{Pope1972,
author = {Pope, JG},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pope/Pope - 1972 - An investigation of the accuracy of virtual population analysis using cohort analysis.pdf:pdf},
journal = {ICNAF Research Bulletin},
title = {{An investigation of the accuracy of virtual population analysis using cohort analysis}},
url = {http://icnaf.nafo.int/res-bull/res-bull-9.pdf{\#}page=65},
year = {1972}
}
@article{Kenchington2014,
abstract = {The 29 estimators of natural mortality (M) that have been proposed for ‘informa- tion-limited' fisheries are reviewed, together with a new alternative presented here. Each is applied to 13 example populations for which well-founded estimates are available of both M and the estimators' parameters. None of the 30 can provide accurate estimates for every species, and none appears sufficiently precise for use in analytical stock assessments, while several perform so poorly as to have no practi- cal utility. If the growth coefficient K has been reliably estimated, either M = 1.5 K or Pauly's long-established estimator can provide useful estimates of M, but they fail with species that have long adult lives after swift juvenile growth, with those that never reach their asymptotic lengths and with species that otherwise deviate from archetypal teleost life histories. If a pre-exploitation maximum observed age (Tmax) can be established, M can be estimated for both teleosts and sharks using M = 4.3/Tmax but that seriously underestimates when the effective sample size (ne) is large and overestimates with species showing pronounced senescence. The new estimator presented here addresses ne but is upset by even mild senescence. Some estimators of M-at-size, particularly ones recently advanced by Gislason et al. and Charnov et al., also show promise but require further examination. It is recom- mended that fisheries scientists measure M by more advanced methods whenever possible. If ‘information-limited' estimators must be used, their uncertainties should be acknowledged and their errors propagated into management advice.},
author = {Kenchington, Trevor J.},
doi = {10.1111/faf.12027},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kenchington/Kenchington - 2014 - Natural mortality estimators for information-limited fisheries.pdf:pdf},
isbn = {9028899251},
issn = {14672979},
journal = {Fish and Fisheries},
keywords = {Information-limited fisheries,Natural mortality},
number = {4},
pages = {533--562},
title = {{Natural mortality estimators for information-limited fisheries}},
volume = {15},
year = {2014}
}
@article{Prager2015,
author = {Prager, Michael H and Consulting, Prager},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prager, Consulting/Prager, Consulting - 2015 - User's Guide for ASPIC Suite, version 7 A Stock–Production Model Incorporating Covariates.pdf:pdf},
title = {{User's Guide for ASPIC Suite, version 7: A Stock–Production Model Incorporating Covariates}},
url = {www.mhprager.com},
year = {2015}
}
@article{Karthik2015,
author = {Karthik, Author and Dyck, Andrew},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Karthik, Dyck/Karthik, Dyck - 2015 - Package ‘ rfisheries '.pdf:pdf},
title = {{Package ‘ rfisheries '}},
year = {2015}
}
@article{Froese2016a,
author = {Froese, R. and Pauly., D.},
title = {{FishBase. World Wide Web electronic publication. www.fishbase.org, ( 06/2016 )}},
year = {2016}
}
@article{Helser1991,
abstract = {This study proposes a new method of estimating the selectivity of gill nets. Using data on the distribution of fish lengths from the catches of various meshes in an experimental gill net, a system of rn equations and n unknown coefficients is simultaneously solved describing the functional relationship of the moments from an assumed mathematical model across mesh size and size-class of fish. The solution to the model is a response surface describing the probability of captureof fish of size-class j in mesh i. This new method is applied to spotted seatrout (Cynscion nebubosus) in coastal Louisiana and used to estimate the relative abundance of the various sine-classes of fish in the population. We suggest that this approach for estimating gillnet selectivity has several advantages over other methods: it is very flexible in terms sf choosing a mathematical model which would best represent the data; it takes ful! advantage of the err{\~{}}pirical data allowing catch information, n,,, to contribute to the final solution both as a function of mesh size and size-class; and it offers simplicity and elegance in its overall iterative least squares approach and is tractable in terms sf assessing the reliability of the parameters and model used. La},
author = {Helser, Thomas E. and Condrey, Richard E. and Geaghan, James P.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Helser, Condrey, Geaghan/Helser, Condrey, Geaghan - 1991 - A new method of estimating gillnet selectivity, with an example for Spotted Seatrout, Cynocion nehulos.pdf:pdf},
isbn = {0706-652X},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
pages = {487--492},
title = {{A new method of estimating gillnet selectivity, with an example for Spotted Seatrout, Cynocion nehulosus}},
url = {http://www.nrcresearchpress.com/doi/pdf/10.1139/f91-062},
volume = {48},
year = {1991}
}
@article{Helidoniotis2013,
abstract = {Field studies that attempt to estimate the mean growth rates of individuals in a population usually yield unbalanced data and various forms of sampling error. If these data are a poor representation of a population, then the estimates of growth rates may also be unrepresentative of the population. We present an assessment of the performance and uncertainty in 4 growth models-the von Bertalanffy, Gompertz, inverse logistic, and Schnute models-fitted to data with various scenarios of sampling error. The performance of each model was determined by comparing highest likelihoods outcomes to known case outcomes. A Monte Carlo simulation framework was used to generate data consisting of 8 typical scenarios of sampling error common in tag-recapture data. Each growth model was evaluated according to 2 metrics: the error rate (i.e., a metric for model uncertainty) and the prediction error (i.e., the accuracy of biological predictions such as age). Results indicate that an inadequate size range in the data (i.e., a lack of juvenile size classes) would often lead to a high error rate. When negative growth increment data are included, the K parameter of the von Bertalanffy model increased, and the L∞ decreased. The inverse logistic model sometimes produced absurd parameter estimates but nevertheless generated the lowest prediction errors. A high prediction error can potentially have far more serious implications to fishery stock assessments than is currently appreciated. Given widespread use of the von Bertalanffy and Gompertz models, selected solely on the basis of model selection criteria, it is clear that greater care and scrutiny are warranted in the selection of growth models in the presence of sampling error.},
author = {Helidoniotis, Fay and Haddon, Malcolm},
doi = {10.2983/035.032.0129},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Helidoniotis, Haddon/Helidoniotis, Haddon - 2013 - Growth Models for Fisheries The Effect of Unbalanced Sampling Error On Model Selection, Parameter Estimati.pdf:pdf},
issn = {0730-8000},
journal = {Journal of Shellfish Research},
keywords = {australia,gompertz,growth,haliotis rubra,inverse logistic,von bertalanffy},
number = {1},
pages = {223--235},
title = {{Growth Models for Fisheries: The Effect of Unbalanced Sampling Error On Model Selection, Parameter Estimation, and Biological Predictions}},
url = {http://www.bioone.org/doi/abs/10.2983/035.032.0129},
volume = {32},
year = {2013}
}
@article{Holst1996,
author = {Holst, Ren{\'{e}} and Madsen, Niels and Moth-Poulsen, Thomas and Fonesca, Paulo and Campos, Aidia},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Holst et al/Holst et al. - 1996 - Manual for gillnet selectivity.pdf:pdf},
pages = {43},
title = {{Manual for gillnet selectivity}},
url = {http://www.constat.dk/Papers/Gillman.pdf},
year = {1996}
}
@article{Huse1999,
abstract = {Selectivity parameters for Greenland halibut (Reinhardtius hippoglossoides, Walbaum) were calculated from trawl and gillnet catches in the Norwegian scientific fisheries for greenland halibut. Within the chosen individual areas and seasons, our data show no trend in length distribution with depth. A trouser-trawl selectivity experiment gave an L50 at 42 cm in a 135 mm codends. A selectivity analysis of the gillnets using a log normal model showed maximum probability of retention for lengths of 46.8-73.5 cm for 140-220 mm stretched meshes. By using expected catch proportions and life history parameters, the selectivity in longline and trawl was shown to be bell-shaped, both gears losing both the smallest and largest fish. Calculated estimated life-history parameters were biased by sampling gears, giving slower growth and larger L??? for females caught in gillnets. The maturation length (M50) of female Greenland halibut was largest in trawl catches, smallest for gillnet catches. The sex ratio in the gillnet catches was shown to be a direct function of mesh size. These analyses will provide a better understanding of possible sampling bias when sampling a stock by means of only one type of gear.},
author = {Huse, Irene and {C. Gundersen}, Agnes and {H. Nedreaas}, Kjell},
doi = {10.1016/S0165-7836(99)00041-7},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Huse, C. Gundersen, H. Nedreaas/Huse, C. Gundersen, H. Nedreaas - 1999 - Relative selectivity of Greenland halibut (Reinhardtius hippoglossoides, Walbaum) by trawls, lo.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Comparative fishing trial,Gillnet,Greenland halibut,Life history,Longline,Selection,Trawl},
number = {1},
pages = {75--93},
title = {{Relative selectivity of Greenland halibut (Reinhardtius hippoglossoides, Walbaum) by trawls, longlines and gillnets}},
volume = {44},
year = {1999}
}
@article{Punt2014,
abstract = {The choice of how to model selectivity differs among approaches to fisheries stock assessment. VPA tends to make only weak assumptions regarding (age-specific) selectivity (asymptotic selectivity and temporal stability of selectivity for the most recent years). In contrast, selectivity is more parametric in "integrated" methods, and can be age-, length-, and age- and length-based. The use of parametric selectivity functions tends to reduce estimation variation because fewer parameters have to be estimated, but incorrect choices for the functional form for selectivity can lead to bias. This paper illustrates effects of poor choices for selectivity on the outcomes of stock assessments, outlines methods for evaluating whether a particular choice for selectivity is appropriate using residual diagnostics, and summarizes current ways to select among alternative functional forms for selectivity. This paper also provides a synthesis of the results of past simulation studies which have explored the ability to correctly parameterize selectivity. ?? 2013 Elsevier B.V.},
author = {Punt, Andr?? E. and Hurtado-Ferro, Felipe and Whitten, Athol R.},
doi = {10.1016/j.fishres.2013.06.003},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Punt, Hurtado-Ferro, Whitten/Punt, Hurtado-Ferro, Whitten - 2014 - Model selection for selectivity in fisheries stock assessments.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {AIC,Asymptotic selectivity,Dome-shaped selectivity,Information criteria model selection,Simulation},
pages = {124--134},
publisher = {Elsevier B.V.},
title = {{Model selection for selectivity in fisheries stock assessments}},
url = {http://dx.doi.org/10.1016/j.fishres.2013.06.003},
volume = {158},
year = {2014}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Pauly 1982.pdf.pdf:pdf},
title = {{Pauly 1982.pdf}}
}
@article{Gulland1971,
abstract = {The fish resources of the ocean form one of the major sources of protein in the world. Though large, these resources are not inexhaustible. The planning of the efficient development of fisheries throughout the world, therefore, requires estimates of the magnitude of the fish stocks being exploited. Such estimates are also useful in providing early warning of when the limits of the resources are being approached, so that the timely implementation of management measures can be considered. The present volume, compiled in the Fishery Resources Division of the Department of Fisheries, is the first comprehensive attempt to estimate the magnitude of these resources, in detail, throughout the world. Inevitably many of the individual estimates presented here will depart from the true value, and some may already, by the time this appears in print, have been shown by the rapid developments in the fisheries to be in error. However, even the present estimates will serve to provide some guidance for the development of fisheries, and the refining and updating of the information contained here is a major element of the progranune of the Department of Fisheries in association with scientists and research institutions throughout the world.},
author = {Gulland, J.A.},
doi = {10.1016/0044-8486(72)90050-6},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gulland/Gulland - 1970 - The fish resources of the ocean.pdf:pdf},
isbn = {0852380550},
issn = {00448486},
journal = {FAO},
keywords = {aquatic animals,benthos,crustacea,fishery management,fishes,mollusca,phytoplankton,saltwater fishes,yields,zooplankton},
pages = {279},
title = {{The fish resources of the ocean}},
url = {http://www.fao.org/docrep/field/003/ab825f/AB825F00.htm{\#}TOC},
year = {1970}
}
@book{Hilborn1992,
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Hilborn, Ray and Walters, Carl J.},
booktitle = {Statewide Agricultural Land Use Baseline 2015},
doi = {10.1017/CBO9781107415324.004},
eprint = {arXiv:1011.1669v3},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hilborn, Walters/Hilborn, Walters - 1992 - Quantitative Fisheries Stock Assessment.pdf:pdf},
isbn = {9788578110796},
issn = {1098-6596},
keywords = {icle},
pmid = {25246403},
title = {{Quantitative Fisheries Stock Assessment}},
volume = {1},
year = {1992}
}
@article{Carl2015,
author = {Carl, Author and Chamberlain, Scott and Temple, Duncan and Wainwright, Peter and Boettiger, Maintainer Carl},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Carl et al/Carl et al. - 2015 - Package ‘ rfishbase '.pdf:pdf},
title = {{Package ‘ rfishbase '}},
year = {2015}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - FSA{\_}0.tar:tar},
title = {{FSA{\_}0}}
}
@article{Gascuel2008,
author = {Gascuel, Didier},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Gascuel/Gascuel - 2008 - Growth rates and apparent growth curves , for yellowfin , skipjack and bigeye tagged and recovered in the Indian Ocean.pdf:pdf},
number = {January},
title = {{Growth rates and apparent growth curves , for yellowfin , skipjack and bigeye tagged and recovered in the Indian Ocean during the IOTTP}},
year = {2008}
}
@article{Fuzzy2015,
author = {Fuzzy, Title and Rule, Logic and Mavridis, Author Constantinos and Athanasiadis, Ioannis N},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Fuzzy et al/Fuzzy et al. - 2015 - Package ‘ FLR '.pdf:pdf},
title = {{Package ‘ FLR '}},
year = {2015}
}
@article{Skern-Mauritzen2015,
author = {Skern-Mauritzen, M. and Ottersen, G. and Handegard, N. O. and Huse, G. and Dings{\o}r, G. E. and Stenseth, N. C. and Kjesbu, O. S.},
journal = {Fish and Fisheries},
title = {{Ecosystem processes are rarely included in tactical fisheries management}},
year = {2015}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - The impact of gillnet selectivity on immature Nile tilapia (Oreochromis niloticus L.) (Pisces Cichlidae) in Lake Ha.docx:docx},
title = {{The impact of gillnet selectivity on immature Nile tilapia (Oreochromis niloticus L.) (Pisces: Cichlidae) in Lake Hawassa, Ethiopia}}
}
@article{Anonymous,
author = {Anonymous},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Anonymous/Anonymous - Unknown - Yield per recruit models.pdf:pdf},
journal = {Presentation},
title = {{Yield per recruit models}}
}
@article{Pauly1986,
author = {Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly/Pauly - 1986 - On improving operation and use of the ELEFAN programs. Part II. Improving the estimation of Linf.pdf:pdf},
journal = {Fishbyte},
title = {{On improving operation and use of the ELEFAN programs. Part II. Improving the estimation of Linf}},
year = {1986}
}
@book{Quinn1999,
address = {New York},
author = {Quinn, T.J. and Deriso, R.B.},
publisher = {Oxford University Press},
title = {{Quantitative fish dynamics}},
year = {1999}
}
@article{Pella1969,
author = {Pella, Jerome J and Tomlinson, Patrick K},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pella, Tomlinson/Pella, Tomlinson - 1969 - A Generalized Stock Production Model.pdf:pdf},
journal = {Inter-Amarican Tropical Tuna Commission},
number = {3},
pages = {421--488},
title = {{A Generalized Stock Production Model}},
volume = {13},
year = {1969}
}
@article{Jensen1981,
abstract = {The normal distribution often is used to describe gill net selection but the normal distribution cannot be integrated in closed form. The logistic distribution, which is a probability distribution similar in shape to the normal distribution, has a probability density function which can be integrated in closed form so that a term for gear selection can be included in the equation describing population size as a function of age. The logistic distribution was applied to the catch curve of Lake Michigan chubs (Coregonus spp.) to adjust it for gill net selection. Yield per 1000 recruits as a function of mean selection age and of fishing mortality was calculated from the adjusted catch curve; these results were compared with yields calculated by conventional methods.},
author = {a.L. Jensen},
doi = {10.1016/0165-7836(81)90017-5},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Jensen/Jensen - 1981 - Adjusting catch curves for gill net selection with the logistic distribution.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
number = {1981},
pages = {155--162},
title = {{Adjusting catch curves for gill net selection with the logistic distribution}},
volume = {1},
year = {1981}
}
@article{Pauly2003a,
author = {Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly/Pauly - 2003 - The relationship between gill surface area and growth performance in fish a generalization of von Bertalanffy's thory of.pdf:pdf},
journal = {Berichte der Deutchen Wissenchaftlichen Kommission fur Meeresforchung},
number = {4},
pages = {1--32},
title = {{The relationship between gill surface area and growth performance in fish: a generalization of von Bertalanffy's thory of growth}},
url = {papers://8f676c60-f047-4e7d-9355-c575d61df01c/Paper/p71},
volume = {28},
year = {2003}
}
@article{Kulmiye2002,
abstract = {Some aspects of the reproductive biology of the thumbprint emperor, Lethrinus harak, (Forssk{\aa}l, 1775) in Kenyan coastal waters were studied from April 1995 to March 1996. Six maturity stages were described for gonad development based on external features. For females, these stages were validated by histological examination of the ovary and by taking oocyte diameter measurements. Size-related discrepancy in male to female sex ratio was observed where males generally predominated in the smaller sizes and females in the larger sizes. Lethrinus harak has a prolonged spawning season extending from October to April with peaks in October and February. The minimum size at which 50 {\%} of males and females attain first sexual maturity was estimated to be 24.2 and 26.4 cm total body length respectively.},
author = {Kulmiye, a J and Ntiba, M J and Kisia, S M},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kulmiye, Ntiba, Kisia/Kulmiye, Ntiba, Kisia - 2002 - Some aspects of the reproductive biology of the thumbprint emperor, Lethrinus harak (Forsskal, 1775), in.pdf:pdf},
isbn = {0856-860X},
journal = {Western Indian Ocean Journal of Marine Science},
keywords = {1775,1995 to march 1996,abstract,for females,for gonad development based,forssk{\aa}l,in kenyan coastal waters,indian ocean,lethrinus harak,maturity stages,maturity stages were described,on external features,reproduction,reproductive biology of the,six,some aspects of the,thumbprint emperor,were studied from april},
number = {2},
pages = {135--144},
title = {{Some aspects of the reproductive biology of the thumbprint emperor, Lethrinus harak (Forsskal, 1775), in Kenyan coastal waters}},
volume = {1},
year = {2002}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Hook selectivity.docx:docx},
title = {{Hook selectivity}}
}
@article{Cadima2003,
abstract = {The manual follows the same order of the lectures in the last course held in IPIMAR (November/December 1997). It starts with an introduction to the mathematical models applied in Fish Stock Assessment and some considerations on the importance of fisheries. The need for a rational management of the fishing resources is then stressed, this being indispensable for an adequate exploitation, aiming at conservation, to occur. The basic assumptions about a model and the concepts of different variation rates of a characteristic in relation to time (or to other characteristics) are presented, highlighting the most important aspects of the simple and exponential linear models which are used in the chapters that follow. After some considerations on the concept of cohort, models for the evolution in time of the number and weight of the individuals that constitute the cohort are developed, including models for the individual growth of the cohort. In the chapter concerning the study of the stock, the fishing pattern and its components are defined, the most used models for the stock?recruitment relation are presented, as well as the short and long term projections of a stock. With regard to fishing resources management, the discussion is focused on the biological reference points (target points, limit points and precautionary points) and fisheries regulation measures. The last chapter, which presents and discusses theoretical models of fish stock assessment, deals with production models (also designated as general production models) and with the long and short–term projections of the catches and biomasses. Finally, the general methods of estimating parameters are described and some of the most important methods are presented, with special relevance to the cohort analysis by age and length. Then a solution of the exercises from the last course held in IPIMAR, is presented by the author and the scientist Manuela Azevedo.},
author = {Cadima, Emydigio L.},
doi = {10.1016/0165-7836(86)90030-5},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Cadima/Cadima - 2003 - Fish Stock Assessment Manual.pdf:pdf},
isbn = {9251045054},
issn = {01657836},
journal = {FAO Technical Paper},
keywords = {fisheries assessment},
number = {393},
pages = {161},
title = {{Fish Stock Assessment Manual}},
url = {http://www.fao.org/docrep/field/003/ab825f/AB825F00.htm{\#}TOC},
year = {2003}
}
@article{Hovgard1999,
author = {Hovg{\aa}rd, Holger and Lassen, Hans},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hovg{\aa}rd, Lassen/Hovg{\aa}rd, Lassen - 1999 - Gillnet selectivity for North Sea Atlantic cod (Gadus morhua) model ambiguity and data quality are related.pdf:pdf},
journal = {{\ldots} Journal of Fisheries {\ldots}},
number = {Holt 1963},
title = {{Gillnet selectivity for North Sea Atlantic cod (Gadus morhua): model ambiguity and data quality are related}},
url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f99-070},
year = {1999}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - y5997e.zip:zip},
title = {y5997e}
}
@article{Andrea2015,
author = {Andrea, Author Lorenzo D and Russo, Tommaso and Parisi, Antonio and Cataudella, Stefano and Andrea, Maintainer Lorenzo D and Area, Assign},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Andrea et al/Andrea et al. - 2015 - Package ‘ vmsbase '.pdf:pdf},
pages = {30},
title = {{Package ‘ vmsbase '}},
year = {2015}
}
@article{Brodziak2011,
author = {Brodziak, Jon and Ianelli, Jim and Lorenzen, Kai and Methot, Richard D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Brodziak et al/Brodziak et al. - 2011 - Estimating Natural Mortality in Stock Assessment Applications.pdf:pdf},
journal = {U.S. Dep. Commer., NOAA Tech. Memo. NMFS-F/SPO-119, 38 p.},
number = {June},
pages = {38},
title = {{Estimating Natural Mortality in Stock Assessment Applications}},
year = {2011}
}
@article{L2015,
author = {L, H Tuncay Kinacig İ},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/L/L - 2015 - by the direct estimation method Ak ı n T . İ LKYAZ.pdf:pdf},
number = {APRIL 2006},
title = {{by the direct estimation method Ak ı n T . İ LKYAZ}},
year = {2015}
}
@misc{Lopez-Veiga1979,
author = {L{\'{o}}pez-Veiga, EC},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/L{\'{o}}pez-Veiga/L{\'{o}}pez-Veiga - 1979 - Fitting von Bertalanffy growth curves in short-lived fish species. A new approach.pdf:pdf},
pages = {179--186},
title = {{Fitting von Bertalanffy growth curves in short-lived fish species. A new approach}},
year = {1979}
}
@article{Society2014,
author = {Society, Royal Statistical},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Society/Society - 2014 - Note on the Number of Plaice at Each Length , in Certain Samples from the Southern Part of the North Sea , 1906 Author.pdf:pdf},
number = {4},
pages = {686--690},
title = {{Note on the Number of Plaice at Each Length , in Certain Samples from the Southern Part of the North Sea , 1906 Author ( s ): T . Edser Source : Journal of the Royal Statistical Society , Vol . 71 , No . 4 ( Dec ., 1908 ), pp . 686-690 Published by : Wile}},
volume = {71},
year = {2014}
}
@article{Anderson2015a,
author = {Anderson, S. C. and Monnahan, C. C. and Johnson, K. F. and Ono, K. and L., Valero J. and J., Cunningham C. and Hurtado-Ferro, F.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Anderson et al/Anderson et al. - 2015 - Package ‘ss3sim'.pdf:pdf},
title = {{Package ‘ss3sim'}},
year = {2015}
}
@article{Kell2007,
author = {Kell, L.T. and Mosqueira, I. and Grosjean, P. and Fromentin, J-M. and Garcia, D. and Hillary, R. and Jardim, E. and Mardle, S. and Pastoors, M.A. and Poos, J.J. and Scott, F. and Scott, R.D.},
journal = {ICES Journal of Marine Science},
pages = {640--646},
title = {{FLR: an open-soiurce framework for the evaluation and development of management strategies.}},
volume = {64},
year = {2007}
}
@book{Series2005,
author = {Series, Computerized Information},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Series/Series - 2005 - stock assessment tools II.pdf:pdf},
isbn = {9251053006},
pages = {52--56},
title = {{stock assessment tools II}},
year = {2005}
}
@article{Kleiber1991,
author = {Kleiber, Pierre},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kleiber/Kleiber - 1991 - Response Surfaces.pdf:pdf},
number = {2},
pages = {45--49},
title = {{Response Surfaces *}},
volume = {9},
year = {1991}
}
@article{Pauly1981,
author = {Pauly, D and David, N},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pauly, Morgan/Pauly, Morgan - 1987 - Length-based methods in fisheries research.pdf:pdf},
journal = {Length-Based Methods in Fisheries {\ldots}},
title = {{ELEFAN I}},
url = {http://core.ac.uk/download/pdf/6515115.pdf{\#}page=372},
year = {1981}
}
@article{Winsor1932,
abstract = {In 1825 Benjamin Gompertz published a paper in the Philosophical Transactions of the Royal Society, "On the Nature of the Function Ex- pressive of the Law of Human Mortality," in which he showed that "if the average exhaustions of a man's power to avoid death were such that at the end of equal infinitely small intervals of time, he lost equal portions of his remaining power to oppose destruction," then the number of sur- vivors at any age x would be given by the equation LX = kge (1) (It is clear that Gompertz means equal proportions, not equal absolute amounts, of the "power to oppose destruction.") The Gompertz curve was for long of interest only to actuaries. More recently, however, it has been used by various authors as a growth curve, both for biological and for economic phenomena. It is the purpose of the present note to consider some of the mathematical properties of this curve, and to indicate to some extent its usefulness and its limitations as a growth curve.},
author = {Winsor, C P},
doi = {10.1073/pnas.18.1.1},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Winsor/Winsor - 1932 - The Gompertz Curve as a Growth Curve.pdf:pdf},
isbn = {0027-8424 (Print)
0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc Natl Acad Sci U S A},
number = {1},
pages = {1--8},
pmid = {16577417},
title = {{The Gompertz Curve as a Growth Curve.}},
volume = {18},
year = {1932}
}
@article{Model,
author = {Model, T H E Cohort},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Model/Model - Unknown - 4 the Population Model.pdf:pdf},
number = {1},
pages = {8--22},
title = {{4 the Population Model}}
}
@article{Tukey1958,
author = {Tukey, J},
journal = {Annals of Mathematical Statistics},
pages = {614},
title = {{Bias and confidence in not quite large samples}},
volume = {29},
year = {1958}
}
@article{Wetherall1987,
author = {Wetherall, J. A. and Polovina, J. J. and Ralston, S.},
journal = {ICLARM Conference Proceedings},
pages = {pp. 53--74},
title = {{Estimating growth and mortality in steady-state fish stocks from length-frequency data}},
volume = {13},
year = {1987}
}
@article{Giannetto2014,
abstract = {Key-words: growth, gill-net selectivity, alien species, euthrophic lake, fisheries management The analysis of catch selectivity of fishing equipment is a crucial step for the management of alien species in freshwater ecosystems. Roach Ru-tilus rutilus was introduced in many waterways in Italy often becoming the dominant species of the fish community and it is now considered po-tential pest. In Piediluco lake the species was first found in 2004 and its abundance has increased at a level that creates concern for the other fish species present in the lake. The growth of R. rutilus and the selectivity of gill-nets on its population were examined in Piediluco lake by analysing the selectivity of gill-nets of different mesh size. Sampling was conducted from January 2011 to October 2012 by means of gill-nets of different-sized mesh (8, 10, 12.5, 15.5, 19.5, 24, 28, 35, 45 and 55 mm). The results showed that R. rutilus in Piediluco lake had a growth faster and higher than in many other lake environments. The results of gill-nets selectivity gave important information to design a plan to control this species and confirmed that the use of suitable fishing techniques could be useful to manage the population of this alien species in Piediluco lake as well as in other similar environments. R{\'{E}}SUM{\'{E}} S{\'{e}}lectivit{\'{e}} en taille des filets maillants et croissance du gardon Rutilus rutilus (Linnaeus, 1758), une esp{\`{e}}ce exotique au lac de Piediluco (Italie) Mots-cl{\'{e}}s : croissance, s{\'{e}}lectivit{\'{e}}, filet maillant, esp{\`{e}}ce exotique, lac eutrophe, gestion des p{\^{e}}ches L'analyse de la s{\'{e}}lectivit{\'{e}} des captures du mat{\'{e}}riel de p{\^{e}}che est une {\'{e}}tape cruciale pour la gestion des esp{\`{e}}ces exotiques dans les {\'{e}}cosyst{\`{e}}mes d'eau douce. Le gardon Rutilus rutilus a {\'{e}}t{\'{e}} introduit dans de nombreux cours d'eau en Italie, devenant souvent l'esp{\`{e}}ce dominante de la communaut{\'{e}} de pois-sons et il est maintenant consid{\'{e}}r{\'{e}} comme nuisible potentiel. Dans le lac de Piediluco l'esp{\`{e}}ce a {\'{e}}t{\'{e}} d{\'{e}}couverte en 2004 et son abondance a augment{\'{e}} {\`{a}} un niveau qui suscite des inqui{\'{e}}tudes pour les autres esp{\`{e}}ces de poissons pr{\'{e}}sents dans le lac. La croissance de R. rutilus et la s{\'{e}}lectivit{\'{e}} des filets maillants sur la population ont {\'{e}}t{\'{e}} examin{\'{e}}es au lac de Piediluco par l'ana-lyse de la s{\'{e}}lectivit{\'{e}} des filets maillants de maillages diff{\'{e}}rents. L'{\'{e}}chantillon-nage a {\'{e}}t{\'{e}} effectu{\'{e}} de janvier 2011 {\`{a}} octobre 2012 au moyen de filets maillants de diff{\'{e}}rentes mailles (8, 10, 12.5, 15.5, 19.5, 24, 28, 35, 45 et 55 mm). Les r{\'{e}}sultats ont montr{\'{e}} que R. rutilus du lac de Piediluco a connu une croissance},
author = {Giannetto, D and Carosi, A and Ghetti, L and Pompei, L and Viali, P and Lorenzoni, M},
doi = {10.1051/kmae/2014001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Giannetto et al/Giannetto et al. - 2014 - Size selectivity of gill-nets and growth of roach Rutilus rutilus (Linnaeus, 1758) an alien species in Piedilu.pdf:pdf},
issn = {1961-9502},
journal = {Knowledge and Management of Aquatic Ecosystems},
pages = {1--13},
title = {{Size selectivity of gill-nets and growth of roach Rutilus rutilus (Linnaeus, 1758) an alien species in Piediluco lake (Italy)}},
url = {http://www.kmae-journal.org},
volume = {413},
year = {2014}
}
@book{Isaac1990a,
author = {Isaac, Victoria J.},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Isaac/Isaac - 1990 - The Accuracy of Some Length-Based Methods for Fish Population Studies.pdf:pdf},
isbn = {9711022869},
pages = {93},
title = {{The Accuracy of Some Length-Based Methods for Fish Population Studies}},
year = {1990}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Screen Shot 2015-11-15 at 19.png:png},
title = {{Screen Shot 2015-11-15 at 19}}
}
@article{Ault2005a,
abstract = {Simulation and empirical analyses were conducted to evaluate the utility and robustness of average length (Lbar) of animals in the exploited population as an estimator of fishing mortality (F), and therefore as an indicator of exploitation status for Florida coral-reef fish. Simulation results showed that the Lbar estimator of fishing mortality was relatively insensitive to trends in recruitment, and demonstrated favourable properties for detecting statistical differences between sustainable and non-sustainable rates of exploitation. Rates of F estimated from fishery-dependent size composition data were comparable to F estimates from catch-and-effort time-series. Average length was also estimated from fishery-independent diver surveys for 22 species in the exploited snapper-grouper complex. A majority of snapper-grouper species are currently fished unsustainably in the Florida Keys, though overfishing appears most severe for long-lived, slow-growing fish. {\textcopyright} 2004 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.},
author = {Ault, Jerald S. and Smith, Steven G. and Bohnsack, James A.},
doi = {10.1016/j.icesjms.2004.12.001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Ault, Smith, Bohnsack/Ault, Smith, Bohnsack - 2005 - Evaluation of average length as an estimator of exploitation status for the Florida coral-reef fish commu.pdf:pdf},
isbn = {1054-3139},
issn = {10543139},
journal = {ICES Journal of Marine Science},
keywords = {Average size,Coral-reef fish,Exploitation,Florida Keys},
number = {3},
pages = {417--423},
title = {{Evaluation of average length as an estimator of exploitation status for the Florida coral-reef fish community}},
volume = {62},
year = {2005}
}
@article{Hurtado-Ferro2014,
abstract = {There is widespread recognition that spatial structure is important for fisheries stock assessment, and several efforts have been made to incorporate spatial structure into assessment models. However, most studies exploring the impact of ignoring spatial structure in stock assessments have developed population models with multiple subpopulations, rather than exploring the impact spatial dynamics may have on performance of non-spatially structured assessment methods. Furthermore, the data available for stock assessments usually do not include tagging or other data necessary to estimate movement rates. One solution to this problem is to include several fleets, each with a different selectivity pattern to represent availability, within a spatially-aggregated assessment method. In this study, the impacts of ignoring spatial structure, and the effectiveness of using multiple selectivity patterns as a proxy for spatial structure, are evaluated for the northern subpopulation of Pacific sardine (or California sardine; Sardinops sagax). A spatially-explicit operating model is used to explore three spatial factors: the existence of size-dependent seasonal migrations across large geographical areas, the influx of another stock into the area of the assessed stock, and the occurrence of recruitment outside the area where it is assumed to occur. Two other factors related to data were evaluated: data availability and data collection design. The assessment model (AM) is based on the 2010 stock assessment for Pacific sardine, implemented in Stock Synthesis, and includes two seasons per year and six fleets, each with a different selectivity pattern. Ignoring spatial structure is found to negatively impact estimation performance, with seasonal movement having the largest impact. The AM compensates for ignoring movement and spatial structure by adjusting the selectivity patterns, but selectivity alone is not able to account for all biases caused by spatial structure. ?? 2013 Elsevier B.V.},
author = {Hurtado-Ferro, Felipe and Punt, Andre E. and Hill, Kevin T.},
doi = {10.1016/j.fishres.2013.10.001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hurtado-Ferro, Punt, Hill/Hurtado-Ferro, Punt, Hill - 2014 - Use of multiple selectivity patterns as a proxy for spatial structure.pdf:pdf},
isbn = {0165-7836},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Pacific sardine,Selectivity,Spatial structure,Stock Synthesis,Stock assessment},
pages = {102--115},
publisher = {Elsevier B.V.},
title = {{Use of multiple selectivity patterns as a proxy for spatial structure}},
url = {http://dx.doi.org/10.1016/j.fishres.2013.10.001},
volume = {158},
year = {2014}
}
@misc{,
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Unknown/Unknown - Unknown - Tamuara and Honma 1977.pdf.pdf:pdf},
title = {{Tamuara and Honma 1977.pdf}}
}
@book{Hay2005,
author = {Hay, Clinton J and N{\ae}sje, Tor F and Thorstad, Eva B},
booktitle = {NINA Report 325},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hay, N{\ae}sje, Thorstad/Hay, N{\ae}sje, Thorstad - 2005 - Fish populations, gill net catches and gill net selectivity in the Kunene River, Namibia.pdf:pdf},
isbn = {{\textless}null{\textgreater}},
title = {{Fish populations, gill net catches and gill net selectivity in the Kunene River, Namibia}},
year = {2005}
}
@article{Brey1986,
author = {Brey, T and Pauly, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Brey, Pauly/Brey, Pauly - 1986 - A user's guide to ELEFAN 0, 1 and 2 (revised and expandedversion).pdf:pdf},
journal = {Berichte des Institut f{\"{u}}r Meereskunde an der Universit{\"{a}}t Kiel},
number = {177},
pages = {77},
title = {{A user's guide to ELEFAN 0, 1 and 2 (revised and expandedversion)}},
volume = {149},
year = {1986}
}
@article{Grundlagen1973,
author = {Grundlagen, I},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Grundlagen/Grundlagen - 1973 - Zur Mathematik des tierischen Wachstums.pdf:pdf},
pages = {509--550},
title = {{Zur Mathematik des tierischen Wachstums}},
volume = {550},
year = {1973}
}
@article{Salvanes1991a,
abstract = {The present study analyses the selectivity for cod in two trammel-nets (three-wall nets) and one gillnet (single-wall net) used during an experimental cod fishery conducted monthly from october 1985 to December 1988 in a Norwegian fjord. It is part of a cod enhancement experiment conducted in the fjord. The three nets were grouped and utilized to sample the wild cod population. In addition, the gillnet and one trammel-net were utilized to sample a tagged group of cod with a known length composition. Relative selectivity curves were estimated indirectly for the two trammel-nets by comparing the catches of each length class within the length range 18-58 cm. Absolute selectivity curves were estimated directly for the gillnet and one trammel-net for the length range 15.0-22.0 cm. These were utilized to verify the indirectly estimated curves. The trammel-net selectivity curves obtained were used to provide an estimate for the true length-frequency distribution of cod in the fjord. Finally, it was tested whether a group of the three nets may be utilized as a unit effort to provide approximate random samples from the population. {\textcopyright} 1991.},
author = {Salvanes, Anne Gro Vea},
doi = {10.1016/0165-7836(91)90080-Y},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Salvanes/Salvanes - 1991 - The selectivity for cod (Gadus morhua L.) in two experimental trammel-nets and one gillnet.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
number = {3-4},
pages = {265--285},
title = {{The selectivity for cod (Gadus morhua L.) in two experimental trammel-nets and one gillnet}},
volume = {10},
year = {1991}
}
@article{Nelson2016,
author = {Nelson, Gary A. Nelson},
title = {{fishmethods: Fishery Science Methods and Models in R. R package version 1.10-0. https://CRAN.R-project.org/package=fishmethods}},
year = {2016}
}
@article{Millar1992a,
abstract = {A conditional maximum likelihood model is used to estimate the size-selectivity of trawls, gillnets, and hooks when the data are obtained by simultaneous fishing with meshes or hooks of different size and/or shape. Size-selectivity is expressed here by the selection curve, r(l), the probability that a fish of length 1, if contacting the gear, will be retained (caught). In many selectivity studies r(l) is fitted either by eye, by heuristic means, or by improper application of generalized linear models. Then it is not possible to make legitimate statistical inference about r(l), or about assessments of the state of the fishery if those assessments use r(l). It is shown here that by conditioning on the total catch, selectivity data can be modeled as binary data, or polytomous data on interval scales. Application of the model to trawl and hook data demonstrates that selection curves can be fitted using generalized linear models, which may require nonstandard link functions or link functions with parameter},
author = {Millar, Russell B.},
doi = {10.1080/01621459.1992.10476250},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Millar/Millar - 1992 - Estimating the size-selectivity of fishing gear by conditioning on the total catch.pdf:pdf},
isbn = {0162-1459},
issn = {0162-1459},
journal = {Journal of the American Statistical Association},
keywords = {conditional maximum likelihood,fishing gear,generalized linear models,logistic curves,poisson totals},
number = {420},
pages = {962--968},
title = {{Estimating the size-selectivity of fishing gear by conditioning on the total catch}},
url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1992.10476250},
volume = {87},
year = {1992}
}
@article{Fujimori2001a,
abstract = {A maximum likelihood method of estimating gillnet selectivity when data are obtained by gillnet fleets consisting of several nets of differing mesh size is presented in this paper. The SELECT model is expanded by application of the relative length (i.e. the ratio of fish length to mesh size) to obtain a master curve of gillnet selectivity. Four kinds of functional model, normal, lognormal, skew-normal and bi-normal are fitted to the data. In addition, two cases in which the relative fishing intensity is either estimated or fixed by catch effort are compared. The bi-normal model has the lower model deviance regardless of whether the relative fishing intensity is estimated or not. The estimation of relative fishing intensity by catch effort is also examined in which the estimates of the parameter of the SELECT model are compared with the catch effort as determined by the number of nets of each mesh size used. For the bi-normal model these quantities compare well. Thus, it is concluded that this method gives reliable estimates even if data for each mesh size is obtained with different catch efforts.},
author = {Fujimori, Yasuzumi and Tokai, Tadashi},
doi = {10.1046/j.1444-2906.2001.00301.x},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Fujimori, Tokai/Fujimori, Tokai - 2001 - Estimation of gillnet selectivity curve by maximum likelihood method(2).pdf:pdf},
isbn = {0919-9268},
issn = {09199268},
journal = {Fisheries Science},
keywords = {Bi-normal,Catch effort,Gillnets,Maximum likelihood method,SELECT model,Selectivity curve},
number = {4},
pages = {644--654},
title = {{Estimation of gillnet selectivity curve by maximum likelihood method}},
volume = {67},
year = {2001}
}
@article{Ehrhardt1992,
abstract = {We performed an assessment of the length-based total mortality model of Beverton and Holt, assuming that catch length-frequency distributions in tropical artisanal fisheries are constrained by (1) the selective properties of multiple gears used and (2) the spatiotemporal availabilities of certain size classes of fish to operationally restricted fleets. Positive bias always resulted with the Beverton and Holt estimator of Z (total mortality); this estimator assumes an infinite exploitable life span. Estimates of Z were unreasonably biased when exploitable life spans were 50{\%} or less of the biological life span of the species considered in the analyses. Biases were larger at lower levels of fishing mortality rates. We developed a new method from a truncated equation for average fish length. It considers length at first capture and the maximum retainable length actually observed in the fishery catch. The method has no explicit solution for Z, so we used numerical methods to provide its solution. The new estimator has zero bias at equilibrium. We determined variance of the new Z-estimator by bootstrap techniques.},
author = {Ehrhardt, Nelson M. and Ault, Jerald S.},
doi = {10.1577/1548-8659(1992)121<0115:AOTLMM>2.3.CO;2},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Ehrhardt, Ault/Ehrhardt, Ault - 1992 - Analysis of Two Length-Based Mortality Models Applied to Bounded Catch Length Frequencies.pdf:pdf},
isbn = {0002-8487},
issn = {0002-8487},
journal = {Transactions of the American Fisheries Society},
pages = {115--122},
title = {{Analysis of Two Length-Based Mortality Models Applied to Bounded Catch Length Frequencies}},
volume = {121},
year = {1992}
}
@article{Carruthers2016a,
author = {Carruthers, Tom and Hordyk, Adrian},
title = {{DLMtool: Data-Limited Methods Toolkit. R package version 3.2.2.}},
url = {https://cran.r-project.org/package=DLMtool},
year = {2016}
}
@article{Hoenig1983,
author = {Hoenig, J. M.},
journal = {Fish. Bull.},
pages = {898--903},
title = {{Empirical use of longevity data to estimate mortality rates}},
volume = {82},
year = {1983}
}
@article{Balan1963,
author = {Balan, V},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Balan/Balan - 1963 - Biology of the silver belly, Leiognathus bindus (Val). of the Calicut coast.pdf:pdf},
journal = {Indian Journal of Fisheries},
number = {1},
pages = {118--134},
title = {{Biology of the silver belly, Leiognathus bindus (Val). of the Calicut coast}},
volume = {10},
year = {1963}
}
@article{Alexander2014,
author = {Alexander, Karen A and Heymans, Johanna J and Magill, Shona and Tomczak, Maciej T and Holmes, Steven J and Wilding, Thomas A},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Alexander et al/Alexander et al. - 2014 - Marine Science.pdf:pdf},
keywords = {cod,ecopath with ecosim,haddock,seals,shelf ecosystem model,whiting},
title = {{Marine Science}},
year = {2014}
}
@article{Kolding2014a,
abstract = {This chapter explores the relationship between small-scale fisheries and resource conservation from a governance perspective. We outline first the significance of small-scale fisheries, particularly in developing countries, while highlighting the serious lack of data, resulting in narratives inherited from industrial fisheries, often with very poor relevance for small-scale fisheries. Current governance structures are then described. Many small-scale fisheries are characterized by self-governing mechanisms that have significant conservation value. The sector is vulnerable however, and under increasing pressure. The push for governance reforms, entailing a two-pronged approach of area closures and effort control, usually results in further marginalization and increased conflicts. The reluctance to conform to Western-inspired management models makes small-scale fishers subject to a negative image, particularly for using indiscriminate fishing methods. Recent findings however challenge the mainstream fisheries narratives and suggest that small-scale fishers' exploitation pattern often might be closer to an ecosystem approach than conventional selective fisheries},
author = {Kolding, J. and Bene, C. and Bavinck, M.},
doi = {10.1002/9781118392607.ch22},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Kolding, Bene, Bavinck/Kolding, Bene, Bavinck - 2014 - Small-scale fisheries Importance, vulnerability and deficient knowledge.pdf:pdf},
isbn = {9781118392607},
journal = {Governance of Marine Fisheries and Biodiversity Conservation: Interaction and Co-evolution},
keywords = {Industrial fisheries,Resource conservation,Small-scale fisheries (SSF)},
pages = {317--331},
title = {{Small-scale fisheries: Importance, vulnerability and deficient knowledge}},
year = {2014}
}
@article{Mildenberger2016,
author = {Mildenberger, Tobias K. and Taylor, Marc H. and Wolff, Matthias},
journal = {Methods in Ecology and Evolution},
title = {{TropFishR: An R package for fisheries analysis with length-frequency data}},
url = {https://doi.org/10.6084/m9.figshare.4212975.v1},
year = {2016}
}
@article{Hordyk2016,
abstract = {{\textcopyright} 2016, Canadian Science Publishing. All rights reserved.Selectivity in fish is often size-dependent, which results in differential fishing mortality rates across fish of the same age, an effect known as "Lee's Phenomenon". We extend previous work on using length composition to estimate the spawning potential ratio (SPR) for data-limited stocks by developing a computationally efficient length-structured per-recruit model that splits the population into a number of subcohorts, or growth-type-groups, to account for size-dependent fishing mortality rates. Two simple recursive equations, using the life history ratio of the natural mortality rate to the von Bertalanffy growth parameter (M/K), were developed to generate length composition data, reducing the complexity of the previous approach. Using simulated and empirical data, we demonstrate that ignoring Lee's Phenomenon results in overestimates of fishing mortality and negatively biased estimates of SPR. We also explored the behaviour of the model under various scenarios, including alternative life history strategies and the presence of size-dependent natural mortality. The model developed in this paper may be a useful tool to estimate the SPR for data-limited stock where it is not possible to apply more conventional methods.},
author = {Hordyk, Adrian and Ono, K. and Prince, J. D. and Walters, Carl J.},
doi = {10.1139/cjfas-2015-0422},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Hordyk et al/cjfas-2015-0422.pdf:pdf},
isbn = {5602235426},
issn = {0706-652X},
journal = {Access},
keywords = {Life histoy,Stock assessment,models,mortality,size distribution},
number = {May},
pages = {1--22},
title = {{A simple length-structured model based on life history ratios and incorporating size-dependent selectivity: application to spawning potential ratios for data-poor stocks}},
volume = {13},
year = {2016}
}
@article{Clay,
author = {Clay, D},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Clay/Clay - 1981 - A New Technique for Estimation of Gillnet Selectivity and Re-analysis of Data for Several Fish Species.pdf:pdf},
number = {1},
pages = {7--22},
title = {{A New Technique for Estimation of Gillnet Selectivity and Re-analysis of Data for Several Fish Species}},
year = {1981}
}
@article{Then2015,
author = {Then, Amy Y. and Hoenig, John M. and Hall, Norman G. and Hewitt, David A.},
doi = {10.1093/icesjms/fst034},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Then et al/Then et al. - 2015 - Evaluating the prodicitve performance of emiprical estimators of natural mortality rate using information on over 2.pdf:pdf},
isbn = {4690786631},
issn = {10543139},
journal = {ICES Journal of Marine Science},
keywords = {Aggregation,bio-acoustics,density,mysids,net sampling,patchiness,size-assortation,swarm},
number = {1},
pages = {82--92},
title = {{Evaluating the prodicitve performance of emiprical estimators of natural mortality rate using information on over 200 fish species}},
volume = {72},
year = {2015}
}
@article{Pelletier1990,
abstract = {Fish stock assessment makes widespread use of Virtual Population Analysis (VPA) and long-term equilibrium prediction models. Although there have been some statistical investigations about the properties of VPA results, apparently there are no complete analyse about predictions statistical and numerical behaviour. However, management decisions generally rely upon production forecasts. This paper compares stability properties of VPA and the yield per recruit model with regard to various errors concerning all the input parameters. Robustness is assessed by means of first-order sensitivities whereas variances are inferred from delta-method estimators. Sensitivity of yield per recruit appears to be mainly due to terminal mortality rate and age-specific weights, and to a lesser extent, the catches and natural mortality. Mean values of the input parameters were also found to influence the model's behaviour. A complete estimation of variances would require a variance-covariance matrix for weights at age and terminal fishing mortality rates. Sensitivies and variances are complementary in that the first quality the absolute robustness of the modesl whereas the second show model robustness in relation to the dimensioned interval of variation of each input parameter. If variances were available for all parameters, yield per recruit estimates could be taken into account for fisheries management decisions},
author = {Pelletier, D},
doi = {10.1051/alr:1990001},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Pelletier/ypr sensitivtiy analysis.pdf:pdf},
issn = {0990-7440},
journal = {Aquatic Living Resources},
keywords = {19130,Age,Assessment,Behaviour,Catch,Catches,Error,Estimators,Fish stock,Fisheries,Fishery,Fishing mortality,Forecast,Long term,Management,Model,Modelling,Models,Mortality,Mortality rates,Natural mortality,Parameters,Population analysis,Prediction,Production,Sensitivity,Stock assessment,VPA,Variance estimators,Variation,Yield,Yield per recruit,Yield-per-recruit,Yield-per-recruit model,errors,fish,fisheries management,mortality rate,population,properties,stability,stock,virtual population analysis},
number = {1},
pages = {1--12},
title = {{Sensitivity and variance estimators for virtual population analysis and the equilibrium yield per recruit model}},
volume = {3},
year = {1990}
}
@article{Prince2015,
abstract = {The theoretical basis of a new approach to data poor fisheries assessment, length-based assessment of spawning potential ratio, has been recently published. This paper describes its first application over two years to assess 12 of the 15 most numerous species of Indo-Pacific coral reef fish in Palau. This study demonstrates the techniques applicability to small-scale data-poor fisheries and illustrates the type of data required, and the assessment's outputs. A methodology is developed for extending the principles of Beverton–Holt Life History Invariants to use the literature on related species within the Indo-Pacific reef fish assemblage to ‘borrow' the information needed to parameterize assessments for Palau's poorly studied stocks. While the assessments will continue to be improved through the collection of more size and maturity data, and through further synthesis of the literature, a consistent and coherent picture emerges of a heavily fished assemblage with most assessed species having SPR{\textless}20{\%} and many {\textless}10{\%}. Beyond the technical aspects of this study, the relative simplicity of the data being collected and the underlying concept of spawning potential facilitated the involvement of fishers in collecting their own data and community ownership of the results.},
author = {Prince, Jeremy and Victor, Steven and Kloulchad, Valentino and Hordyk, Adrian},
doi = {10.1016/j.fishres.2015.06.008},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prince et al/Prince et al 2015 Palauan Reef Fish assessments.pdf:pdf},
issn = {01657836},
journal = {Fisheries Research},
keywords = {Data poor assessment,Indo-Pacific reef fish,Length based SPR,Spawning potential ratio},
number = {July},
pages = {42--58},
publisher = {Elsevier B.V.},
title = {{Length based SPR assessment of eleven Indo-Pacific coral reef fish populations in Palau}},
url = {http://www.sciencedirect.com/science/article/pii/S0165783615001885},
volume = {171},
year = {2015}
}
@article{Costello2012,
abstract = {Recent reports suggest that many well-assessed fisheries in developed countries are moving toward sustainability. We examined whether the same conclusion holds for fisheries lacking formal assessment, which comprise {\textgreater}80{\%} of global catch. We developed a method using species' life-history, catch, and fishery development data to estimate the status of thousands of unassessed fisheries worldwide. We found that small unassessed fisheries are in substantially worse condition than assessed fisheries, but that large unassessed fisheries may be performing nearly as well as their assessed counterparts. Both small and large stocks, however, continue to decline; 64{\%} of unassessed stocks could provide increased sustainable harvest if rebuilt. Our results suggest that global fishery recovery would simultaneously create increases in abundance (56{\%}) and fishery yields (8 to 40{\%}).},
author = {Costello, Christopher and Ovando, Daniel and Hilborn, Ray and Gaines, Steven D and Deschenes, Olivier and Lester, Sarah E},
doi = {10.1126/science.1223389},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Costello et al/Costello et al. - 2012 - Status and solutions for the world's unassessed fisheries.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Animals,Conservation of Natural Resources,Conservation of Natural Resources: statistics {\&} nu,Fisheries,Fisheries: standards,Fisheries: statistics {\&} numerical data,Multivariate Analysis,Seafood,Seafood: standards,Seafood: statistics {\&} numerical data},
month = {oct},
number = {6106},
pages = {517--20},
pmid = {23019613},
title = {{Status and solutions for the world's unassessed fisheries.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23019613},
volume = {338},
year = {2012}
}
@article{Prager1988,
abstract = {Virtual population analysis (VPA) is widely used in fish stock assessment. However, VPA results are generally presented as point estimates, without error variance. Using numerical methods, we estimated that total variance of historical (1929-65) biomass estimates of mackerel, Scomber japonicus, off southern California [USA]. In the years before 1940, coefficients of variation (CV's) approached 100{\%}; later, when weights at age and the age structure of the catch were better known, the CV's were about 25{\%}. Most of the variability derives from uncertainties in estimates of natural mortality (M) and of weights at age. We also developed dimensionless coefficients (sensitivities) to examine the effects of errors in the inputs on the VPA biomass estimates. The largest sensitivities were to M and the total catch and varied substantially from year to year. As expected, sensitivity to M decreased with increasing exploitation, and sensitivity to catch increased with increasing exploitation. Using such sensitivities, one could estimate the error in a biomass estimate for a past year when M (or any other input) was thought to be unusually high or low. Thus, retrospective corrections can be made. Also, such sensitivities from an analytic tool for exmaining the properties of VPA, or any quantitative model.},
author = {Prager, M H and Maccall, A D},
doi = {10.1139/f88-063},
file = {:Users/tobiasmildenberger/Documents/Mendeley Desktop/Prager, Maccall/VPA sensitivity.pdf:pdf},
isbn = {0706-652X},
issn = {0706-652X},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
keywords = {(Chordata-General-and-Systematic-Zoology-Pisces),(Developmental-Biology-Embryology-Morphogenesis-Ge,-Aquatic),-Environmental-Biology-Oceanography),Animals-,CC04500 (Mathematical-Biology-and-Statistical-Meth,CC07516 (Ecology-Environmental-Biology-Wildlife-Ma,Chordates-,FISH STOCK ASSESSMENT BIOMASS AGE STRUCTURE QUANTI,Fish-,Nonhuman-Vertebrates,Osteichthyes-: Pisces-, Vertebrata-, Chordata-, An,USA,Vertebrates-},
number = {3},
pages = {539--547},
pmid = {198886025315},
title = {{Sensitivities and Variances of Virtual Population Analysis as Applied to the Mackerel Scomber-Japonicus}},
volume = {45},
year = {1988}
}
