Introducing selfisher: open source software for statistical analyses of fishing gear selectivity
Publication: Canadian Journal of Fisheries and Aquatic Sciences
24 January 2022
Abstract
There is a need to improve fishing methods to select for certain sizes and species while excluding others. Experiments are conducted to quantify selectivity of fishing gears and how variables such as gear design (e.g., mesh size, mesh shape), environmental parameters (e.g., light, turbidity, substrate) or biological parameters (e.g., fish condition) alter selectivity; the resulting data need to be analyzed using specialized statistical methods in many cases. Here, we present a new tool for analyzing this type of data: an R package named “selfisher”. It allows estimating multiple fixed effects (e.g., fish length, total catch weight, environmental variables) and random effects (e.g., haul). A bootstrapping procedure is also provided. We demonstrate its use via four case studies, including (A) covered codend analyses of four gears, (B) a paired gear study with numerous covariates, (C) a catch comparison study of unpaired hauls of gillnets and (D) a catch comparison study of paired hauls using polynomials and splines. This software will make it easier to model selectivity, teach statistical methods, and make analyses more repeatable.
Résumé
Il est nécessaire d’améliorer les méthodes de pêche pour qu’elles sélectionnent certaines tailles et espèces et en excluent d’autres. Des expériences sont menées afin de quantifier la sélectivité d’engins de pêche et l’influence de variables comme la conception des engins (p. ex. taille et forme des mailles) ou des paramètres environnementaux (p. ex. lumière, turbidité, substrat) ou biologiques (p. ex. embonpoint des poissons) sur la sélectivité; dans de nombreux cas, les données qui en découlent doivent être analysées par des méthodes statistiques spécialisées. Nous présentons un nouvel outil pour l’analyse de ce type de données, un progiciel R appelé « selfisher ». Il permet l’estimation de multiples effets fixes (p. ex. longueur des poissons, masse totale des prises, variables environnementales) et aléatoires (p. ex. trait). Une procédure d’amorçage est également présentée. Nous démontrons comment l’utiliser par l’entremise de quatre études de cas dont (A) l’analyse de culs de chalut couverts de quatre engins, (B) une étude d’engins jumelés comprenant de nombreuses variables corrélées, (C) une étude de comparaison des prises de traits non jumelés de filets maillants et (D) une étude de comparaison des prises de traits jumelés faisant appel à des polynômes et des splines. Ce logiciel facilitera la modélisation de la sélectivité et l’enseignement de méthodes statistiques et rehaussera la répétabilité des analyses. [Traduit par la Rédaction]
Get full access to this article
View all available purchase options and get full access to this article.
References
Baranov, F.I. 1948. Theory and assessment of fishing gear. In Theory of fishing with gillnets. Chapter 7. In Pishchepromizdat. Moscow. [Translation from Russian by Ontario Dept of Lands, Maple, Ont.]
Bates D., Mächler M., Bolker B., and Walker S. 2015. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67(1): 1–48.
Bolker B.M., Gardner B., Maunder M., Berg C.W., Brooks M., Comita L., et al. 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods Ecol. Evol. 4: 501–512.
Brooks M.E., Kristensen K., van Benthem K.J., Magnusson A., Berg C.W., Nielsen A., et al. 2017. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 9(2): 378–400.
Erickson D.L., Perez-Comas J.A., Pikitch E.K., and Wallace J.R. 1996. Effects of catch size and codend type on the escapement of walleye pollock (Theragra chalcogramma) from pelagic trawls. Fish. Res. 28(2): 179–196.
Ferro R.S.T., Özbilgin H., and Breen M. 2008. The potential for optimizing yield from a haddock trawl fishery using seasonal changes in selectivity, population structure and fish condition. Fish. Res. 94(2): 151–159.
Fournier D.A., Skaug H.J., Ancheta J., Ianelli J., Magnusson A., Maunder M.N., et al. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optim. Methods Softw. 27(2): 233–249.
Fryer R.J. 1991. A model of between-haul variation in selectivity. ICES J. Mar. Sci. 48(3): 281–290.
Fryer R.J., Zuur A.F., and Graham N. 2003. Using mixed models to combine smooth size-selection and catch-comparison curves over hauls. Can. J. Fish. Aquat. Sci. 60(4): 448–459.
He P. 1993. Swimming speeds of marine fish in relation to fishing gears. ICES Mar. Sci. Symp. 196: 183–189.
Herrmann B., Sistiaga M., Rindahl L., and Tatone I. 2017. Estimation of the effect of gear design changes on catch efficiency: methodology and a case study for a Spanish longline fishery targeting hake (Merluccius merluccius). Fish. Res. 185: 153–160.
Holst R. and Revill A. 2009. A simple statistical method for catch comparison studies. Fish. Res. 95(2–3): 254–259.
Kennelly S.J. and Broadhurst M.K. 2021. A review of bycatch reduction in demersal fish trawls. Rev. Fish Biol. Fish. 31: 289–318.
Kristensen K., Nielsen A., Berg C.W., Skaug H., and Bell B.M. 2016. TMB: Automatic Differentiation and Laplace Approximation. J. Stat. Softw. 70(5): 1–21.
Kuk A.Y. 1989. Double bootstrap estimation of variance under systematic sampling with probability proportional to size. J. Stat. Comput. Simul. 31(2): 73–82.
Larsen R.B., Herrmann B., Sistiaga M., Brinkhof J., and Grimaldo E. 2018. Bycatch reduction in the Norwegian deep-water shrimp (Pandalus borealis) fishery with a double grid selection system. Fish. Res. 208: 267–273.
Melli V., Karlsen J.D., Feekings J.P., Herrmann B., and Krag L.A. 2018. FLEXSELECT: counter-herding device to reduce bycatch in crustacean trawl fisheries. Can. J. Fish. Aquat. Sci. 75(6): 850–860.
Melli V., Krag L.A., Herrmann B., and Karlsen J.D. 2019. Can active behaviour stimulators improve fish separation from Nephrops (Nephrops norvegicus) in a horizontally divided trawl codend? Fish. Res. 211: 282–290.
Millar R.B. 1993. Incorporation of between‐haul variation using bootstrapping and nonparametric estimation of selection curves. Fish. Bull. 91: 564–572.
Millar R.B. 1994. Sampling from trawl gears used in sized selectivity experiments. ICES J. Mar. Sci. 51(3): 293–298.
Millar, R.B. 2011. Maximum likelihood estimation and inference: with examples in R, SAS and ADMB. Wiley, London. ISBN: 978-0-470-09482-2.
Millar R.B. and Fryer R.J. 1999. Estimating the size-selection curves of towed gears, traps, nets and hooks. Rev. Fish Biol. Fish. 9(1): 89–116.
Millar R.B., Broadhurst M.K., and Macbeth W.G. 2004. Modelling between-haul variability in the size selectivity of trawls. Fish. Res. 67(2): 171–181.
Miller T. 2013. A comparison of hierarchical models for relative catch efficiency based on paired-gear data for US Northwest Atlantic fish stocks. Can. J. Fish. Aquat. Sci. 70(9): 1306–1316.
Munro P.T. and Somerton D.A. 2001. Maximum likelihood and non-parametric methods for estimating trawl footrope selectivity. ICES J. Mar. Sci. 58(1): 220–229.
Ogden H. 2021. On the error in Laplace approximations of high-dimensional integrals. Stat, 10(1): e380.
O’Neill F.G. and Kynoch R.J. 1996. The effect of cover mesh size and cod-end catch size on cod-end selectivity. Fish. Res. 28(3): 291–303.
O’Neill F.G., Kynoch R.J., Blackadder L., Fryer R.J., Eryaşar A.R., Notti E., and Sala A. 2016. The influence of twine tenacity, thickness and bending stiffness on codend selectivity. Fish. Res. 176: 94–99.
Özbilgin H., Tosunoğlu Z., Tokaç A., and Metin G. 2007. Seasonal variation in the trawl codend selectivity of picarel (Spicare smaris). ICES J. Mar. Sci. 64(8): 1569–1572.
Pérez Roda, M.A., Gilman, E., Huntington, T., Kennelly, S.J., Suuronen, P., Chaloupka, M., and Medley, P. 2019. A third assessment of global marine fisheries discards. FAO Fisheries and Aquaculture Technical Paper No. 633, FAO, Rome.
R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available from http://www.R-project.org/.
Revill A.S. and Holst R. 2004. Reducing discards of North Sea brown shrimp (C. crangon) by trawl modification. Fish. Res. 68: 113–122.
Ryer C.H. and Barnett L.A. 2006. Influence of illumination and temperature upon flatfish reactivity and herding behavior: potential implications for trawl capture efficiency. Fish. Res. 81(2–3): 242–250.
Santos J., Herrmann B., Mieske B., Stepputtis D., Krumme U., and Nilsson H. 2016. Reducing flatfish bycatch in roundfish fisheries. Fish. Res. 184: 64–73.
Santos J., Herrmann B., Stepputtis D., Günther C., Limmer B., Mieske B., et al. 2018. Predictive framework for codend size selection of brown shrimp (Crangon crangon) in the North Sea beam-trawl fishery. PLoS ONE, 13(7): e0200464.
Savina E., Krag L.A., Frandsen R.P., and Madsen N. 2017. Effect of fisher’s soak tactic on catch pattern in the Danish gillnet plaice fishery. Fish. Res. 196: 56–65.
Skalski J.R. and Perez-Comas J. 1993. Nonparametric maximum likelihood estimation of mesh size selectivity. Fish. Res. 18(3–4): 321–334.
Somerton D.A., Weinberg K.L., Goodman S.E., and Chen Y. 2013. Catchability of snow crab (Chionoecetes opilio) by the eastern Bering Sea bottom trawl survey estimated using a catch comparison experiment. Can. J. Fish. Aquat. Sci. 70(12): 1699–1708.
Suuronen P. and Millar R.B. 1992. Size selectivity of diamond and square mesh codends in pelagic herring trawls: only small herring will notice the difference. Can. J. Fish. Aquat. Sci. 49(10): 2104–2117.
Thorson, J. 2020. TMBhelper: Package for basic helper functions that are not worth putting in a specialized contributed package. R package version 1.3.0.
Tokai T., Omoto S., Sato R., and Matuda K. 1996. A method of determining selectivity curve of separator grid. Fish. Res. 27(1–3): 51–60.
Veiga-Malta T., Feekings J., Herrmann B., and Krag L.A. 2019. Industry-led fishing gear development: Can it facilitate the process? Ocean Coast. Manage. 177: 148–155.
Veiga-Malta T., Feekings J.P., Frandsen R.P., Herrmann B., and Krag L.A. 2020. Testing a size sorting grid in the brown shrimp (Crangon crangon Linnaeus, 1758) beam trawl fishery. Fish. Res. 231: 105716.
Walsh S.J. and Hickey W.M. 1993. Behavioural reactions of demersal fish to bottom trawls at various light conditions. ICES Mar. Sci. Symp. 196: 68–76.
Wienbeck H., Herrmann B., Feekings J.P., Stepputtis D., and Moderhak W. 2014. A comparative analysis of legislated and modified Baltic Sea trawl codends for simultaneously improving the size selection of cod (Gadus morhua) and plaice (Pleuronectes platessa). Fish. Res. 150: 28–37.
Wileman, D., Ferro, R.S.T., Fonteyne, R., and Millar, R.B. 1996. Manual of methods of measuring the selectivity of towed fishing gears. ICES Coop. Res. Rep. 215.
Supplementary Material
Supplementary data (cjfas-2021-0099suppla.zip)
- Download
- 1.22 MB
Information & Authors
Information
Published In
Canadian Journal of Fisheries and Aquatic Sciences
Volume 79 • Number 8 • August 2022
Pages: 1189 - 1197
History
Received: 24 April 2021
Accepted: 7 January 2022
Accepted manuscript online: 24 January 2022
Version of record online: 24 January 2022
Copyright
© 2022 The Author(s). Permission for reuse (free in most cases) can be obtained from copyright.com.
Authors
Funding Information
:
We are grateful for funding from the European Maritime and Fisheries Fund (EMFF) and the Ministry of Environment and Food of Denmark (Miljø- og Fødevareministeriet) as part of the projects FastTrack – Sustainable, cost effective and responsive gear solutions under the landing obligation (33112-P-15-013), FastTrack II – Sustainable, cost effective and responsive gear solutions under the landing obligation (33112-P-18-051), and Flexselect – Innovative and Flexible solutions for the Nephrops Fisheries (33113-I-16-068).
Metrics & Citations
Metrics
Other Metrics
Citations
Cite As
Mollie E. Brooks, Valentina Melli, Esther Savina, Juan Santos, Russell Millar, Finbarr Gerard O’Neill, Tiago Veiga-Malta, Ludvig Ahm Krag, and Jordan Paul Feekings. 2022. Introducing selfisher: open source software for statistical analyses of fishing gear selectivity. Canadian Journal of Fisheries and Aquatic Sciences.
79(8): 1189-1197. https://doi.org/10.1139/cjfas-2021-0099
Export Citations
If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.
Cited by
1. Illuminating square meshed panels with white-coloured LED ropes to stimulate escape of undersized fish in beam trawl fisheries
2. The effect of variable light intensity in luminescent-netting pots on the catch of snow crab (Chionoecetes opilio)
3. Effects of codend mesh shape on catch selectivity in bottom trawl
4. Guidelines for Evaluating Artificial Light to Mitigate Unwanted Fisheries Bycatch
5. A Study on the Catch Losses and Mesh Selectivity Related to the Attachment of Marine Mammal Bycatch Reduction Devices on Midwater Trawl Gear
6. Hybrid experimental designs for joint estimation of absolute and relative retention curves for trawl gears
7. Smaller bar spacings in a Nordmøre grid reduces the bycatch of redfish (Sebastes spp.) in the offshore Northern shrimp (Pandalus borealis) fishery of eastern Canada
8. Effects of the implementation of T90 extension and 52 mm square mesh codend on the bottom trawl hake fishery of the north western Mediterranean
9. Improving size selection in the Norwegian red king crab (Paralithodes camtschaticus) fishery through modification to pot design and soak time.
10. Testing of a helix twine off-bottom trawl on Georges Bank
11. Investigating the potential of escape openings and reduced mesh size to optimize snow crab (Chionoecetes opilio) pot catches in the Barents Sea
12. The effects of LED handline attachments on Atlantic cod (Gadus morhua) catch efficacy and bycatch
13. Testing experimental devices in the extension piece to increase the selectivity of bottom trawl in the Nw Mediterranean
View Options
Login options
Check if you access through your login credentials or your institution to get full access on this article.
Subscribe
Click on the button below to subscribe to Canadian Journal of Fisheries and Aquatic Sciences