Welcome to our R-SHINY app
The aim of this app has been to visualize DTU's research vessel Havfisken's data in both time and space.
The development of the script/shiny-app has been conducted through iteration. This includes playing around with the user interface to implement as many different interactions as possible. This way, one can go back to this script any time in the future and reuse and/or update it.
The app is aimed towards anyone interested in easy DATRAS data visualization. These could be scientists, students or other stakeholders. Therefore the code has been made as generic as possible with the aim of the abbility to upload any DATRAS dataset to the shiny-app in the R-CODE. See section "Future work".
App content
The shiny-app is build up around a sidebar menu located on the left side of the app-window. Menu items include the following:
- Background
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Tabboxes containing introduction and information about the Interactivity, Future work and R code.
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Information about the research vessel Havfisken and four different types of trawling gear (Havfisken is equipped for easy exchange of trawl types). According to the DATRAS-data it uses a small TV trawl which, by image inspection, appears like a otter or siene trawl.
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In this section the DATRAS data is visualized. It is possible to choose specific trawl stations (geographically) and plot catch rates for specific species. Furthermore the aim has been to show additional information such as depth, number of trawls and specific species-information.
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Get an overview of the DATRAS datasets for both quarter 1 anf 4 with the possibility to download the files.
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A list of references used in the app.
Andreas Blach Søby & Line Overgaard Bering
Interactivity of R-shiny input and output
The first thing we do is to merge the data for both quarters. This way we can easily choose between quarters later on
Flowcharts showing interactivity for map-output, plot-output, table-output and species-output
How can the app develop?
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The plot with the map needs to be able to show the right longitude and latitudee according to dataset. We can do that by making the longitude and latitude in the map-output in the server cahage with max and min values in the dataset. Fo now it only shows latitude and longitude for Denmark.
Only the 6 most common species are showed. Instead, the species list should be as the species column in the dataset. This was not done as it would take a lot of time to write a description about all species.
A sliderinput for "years" could be useful to change the range of years. This way the user will be able to 'zoom in' on a specific year-range.
There's a lot more data in the DATRAS dataset that could be visalized and analysed in several ways.
Script in R
It's also made possible to run the app as a code-showcase. This will run the app with a sidebar with the script. This way it is easy to see what reacts in the script as it will turn yellow when it reacts. Simply uncomment line 4 in the script.
Havfisken
Use
DTU aqua’s research vessel Havfisken facilitate research and observational tasks in inner danish waters as well as education of students from the master in Aquatic science and technology at DTU. Havfisken is build similar to a modern fishing boat and supplement the larger DTU fishing boat Dana, which solve similar tasks outside danish waters. Observational data collected by Dana and Havfisken are included in ICES databases, advice sheets and therefore also decisions regarding fisheries quotas.
Practical information
Havfisken is 17 meters long and weighs 105 tons. Instead of a storage room, Havfisken contains a laboratory for sample processing, cabins and a meeting room. The lab includes work places, a freezer for sample storage, a fume table and a conveyor belt.
Havfisken is equipped with a system for easy trawl type exchange. An A frame and a crane is attached in the hind of the ship for handling different scientific gear like measuring devices or cameras.
The ship is harbored at Strandby in Northern Jutland (DTU, 2018).
A beam trawl basically consists of a cone shaped net body wich narrows toward the end in a bag to retain catch. The horizontal opening of the net is constructed with a beam of steel or wood and the vertical opening in kept by hoop like constructions of steel. sometimes the beam trawl is equipped with tickler chains that function to disturb fish from the seabed. If used on rough terain the trawl can be equipped with chain matrices rigged between the beam and groundrope to prevent large stones from entering the net. targeted species are mainly flatfish or shrimp (FAO 2022). A beam trawl with tickler chains can generate furrows up to 10 cm deep into the sediment. Overall footprint size of a fishing vessel is defined as the width of a given beam multiplied by the number of beam trawls deployed. Width typically vary between 4 and 12 m and towing speed ranges from 2.5 to 7 knots. Depth of operation is typically conducted at 100 m or shallower (R. Eigaard et al. 2016).
Otter trawl are very heterogenous in desig but generally consists of a cone shaped net narrowing into a bag to retain catch. It consists of two latral wings kept open by horizontally by two otter boards. the verical opening constructed from an extended top panel to prevent fish from excaping upwards is obtained floats or kites. The groundrope which functions as the lower part of the vertical opneing is kept down with weights and is usualy attached to groundgear to protect against wear and help the trwal across terrain. Target species include benthic and demersal species (FAO 2022). Width ranges from 25-250m and towing speed ranges from 2 to 4 knots. Depth of operation can range from 10 to 2500 m. Footprint on the seabed is caterygorized by otter boards wich can dig furrows up to 35 cm deep (the most severe), sweeps and trawl groundgear. (Eigaard et al. 2016).
There are many types of dredges depending og the fishing method. In this case the focus is on boat dregdges, which can be towed behind a boat. They can be split into two categories: dredges that scrape the seafloor surface and dredges that penetrate the sea floor to catch benthic infauna species. Generally a dredge consists of a mouth frame with scraping mechanism like teeths or shearing edge and a holding bag attached. The holding bag can be constructed of metal rings or meshes. Targeted species consist primarily of benthic shelfish like mussels, scallops and oysters (FAO 2022). Typical dredge width ranges from 0.75 to 3 m. Towing speed from 2 to 2.5 knots at somewhat shallow and close to coastal waters. Seafloor impact depends on dredge size and penetration depthR (Eigaard et al. 2016).
Seines consist of a conical netting body, two long wings and a net bag for conatining the catch. An important distinctive trait for seines is the long ropes extending from the wings, which function to encircle a large area and "shepherd" fish towards the netting body as the ship towes the seine. The groundrope is often weighted to keep the seines and net close to the seafloor. Fishing with seines take place from shallow water to depths around 180 m. Length of seines typically vary from 4400 to 7920 m. Impact on seabed is mainly caused from the seine ropes themsleves whereas the seine groundgear only cover a fraction of totalt area fished. Targeted species consist primarily of dimersal fish like species of flat fish, but also somewhat pelagic species like trout (FAO 2022; R. Eigaard et al. 2016).
Area of interest
Change longitude and latitude on sliders
Red points show data selected in chosen area. If there's an error, no data is available and longitude and latitude should be changed.
Plot of mean weight in haul
Mean weight in hauls
The plot shows the mean weight in hauls made within the chosen area and quarter.Click on the plot to see exact year and weight
Observations and depth
References
Cohen, D.M., T. Inada, T. Iwamoto and N. Scialabba, 1990. FAO species catalogue. Vol. 10. Gadiform fishes of the world (Order Gadiformes). An annotated and illustrated catalogue of cods, hakes, grenadiers and other gadiform fishes known to date. FAO Fish. Synop. 125(10). Rome: FAO. 442 p.
Cooper, J.A. and F. Chapleau, 1998. Monophyly and intrarelationships of the family Pleuronectidae (Pleuronectiformes), with a revised classification. Fish. Bull. 96(4):686-726.
FAO 2022. Fishing Gear types. Beam trawls. Technology Fact Sheets. Fisheries and Aquaculture Division [online]. Rome. [Cited Thursday, May 5th 2022]. https://www.fao.org/fishery/en/geartype/305/en
FAO 2022. Fishing Gear types. Boat seines. Technology Fact Sheets. Fisheries and Aquaculture Division [online]. Rome. [Cited Thursday, May 5th 2022]. https://www.fao.org/fishery/en/geartype/203/en
FAO 2022. Fishing Gear types. Single boat bottom otter trawls. Technology Fact Sheets. Fisheries and Aquaculture Division [online]. Rome. [Cited Thursday, May 5th 2022]. https://www.fao.org/fishery/en/geartype/306/en
FAO 2022. Fishing Gear types. Towed dredges. Technology Fact Sheets. Fisheries and Aquaculture Division [online]. Rome. [Cited Thursday, May 5th 2022]. https://www.fao.org/fishery/en/geartype/212/en
Frimodt, C., 1995. Multilingual illustrated guide to the world's commercial coldwater fish. Fishing News Books, Osney Mead, Oxford, England. 215 p.
Muus, B.J. and P. Dahlström, 1974. Collins guide to the sea fishes of Britain and North-Western Europe. Collins, London, UK. 244 p.
Nielsen, J.G., 1986. Pleuronectidae. p. 1299-1307. In P.J.P. Whitehead, M.-L. Bauchot, J.-C. Hureau, J. Nielsen and E. Tortonese (eds.) Fishes of the North-eastern Atlantic and the Mediterranean. UNESCO, Paris. Vol. 3.
Ole R. Eigaard, Francois Bastardie, Mike Breen, Grete E. Dinesen, Niels T. Hintzen, Pascal Laffargue, Lars O. Mortensen, J. Rasmus Nielsen, Hans C. Nilsson, Finbarr G. O’Neill, Hans Polet, David G. Reid, Antonello Sala, Mattias Sköld, Chris Smith, Thomas K. Sørensen, Oliver Tully, Mustafa Zengin, Adriaan D. Rijnsdorp, Estimating seabed pressure from demersal trawls, seines, and dredges based on gear design and dimensions, ICES Journal of Marine Science, Volume 73, Issue suppl_1, January 2016, Pages i27–i43, https://doi.org/10.1093/icesjms/fsv099
Whitehead, P.J.P., 1985. FAO Species Catalogue. Vol. 7. Clupeoid fishes of the world (suborder Clupeoidei). An annotated and illustrated catalogue of the herrings, sardines, pilchards, sprats, shads, anchovies and wolf-herrings. FAO Fish. Synop. 125(7/1):1-303. Rome: FAO.