VMSbase: An R-Package for VMS and logbook data management and analysis in fisheries ecology

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Russo, Tommaso ^a   D'Andrea, Lorenzo ^a   Parisi, Antonio ^b   Cataudella, Stefano ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; DATA CLEANING; DATA ENHANCING; DATA PROCESSING; FISHERY MANAGEMENT; SAMPLE SIZE; VMSBASE; WORKFLOW; ANIMAL; BIODIVERSITY; ECOLOGY; ENVIRONMENTAL PROTECTION; FACTUAL DATABASE; FISH; FISHERY; PHYSIOLOGY;

ANIMALS; BIODIVERSITY; CONSERVATION OF NATURAL RESOURCES; DATABASES, FACTUAL; ECOLOGY; FISHERIES; FISHES; SOFTWARE;

EID: 84903195925     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100195     Document Type: Article

References (60)

1. Witt MJ, Godley BJ (2007) A Step Towards Seascape Scale Conservation: Using Vessel Monitoring Systems (VMS) to Map Fishing Activity. doi:10.1371/journal.pone.0001111.
2. Gerritsen H, Lordan C (2010) Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution. ICES J Mar Sci 68: 245-252. Available: http://icesjms.oxfordjournals.org/cgi/doi/10.1093/icesjms/fsq137. Accessed 30 May 2013.
3. Lambert GI, Jennings S, Hiddink JG, Hintzen NT, Hinz H, et al. (2012) Implications of using alternative methods of vessel monitoring system (VMS) data analysis to describe fishing activities and impacts: 1-12. doi:10.1093/icesjms/ fss018.
4. Russo T, Parisi A, Cataudella S (2013) Spatial indicators of fishing pressure: Preliminary analyses and possible developments. Ecol Indic 26: 141-153. Available: http://linkinghub.elsevier.com/retrieve/pii/ S1470160X12003822. Accessed 7 November 2013.
5. Hintzen NT, Bastardie F, Beare D, Piet GJ, Ulrich C, et al. (2012) VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data. Fish Res 115-116: 31-43. Available:http://dx. doi.org/10.1016/j.fishres.2011.11.007.
6. Acom ICM (2011) ICES WKCPUEFFORT REPORT 2011 commercial CPUE and VMS data in assess- Report of the Workshop on the utility of ment (WKCPUEFFORT): 5-7.
7. Coll M, Cury P, Azzurro E, Bariche M, Bayadas G, et al. (2013) The scientific strategy needed to promote a regional ecosystem-based approach to fisheries in the Mediterranean and Black Seas. Rev Fish Biol Fish. Available: http://link.springer.com/10.1007/s11160-013-9305-y. Accessed 15 November 2013.
8. Russo T, Parisi A, Cataudella S (2011) New insights in interpolating fishing tracks from VMS data for different métiers. Fish Res 108: 184-194. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0165783610003450. Accessed 4 September 2012.
9. Russo T, Parisi A, Prorgi M, Boccoli F, Cignini I, et al. (2011) When behaviour reveals activity: Assigning fishing effort to métiers based on VMS data using artificial neural networks. Fish Res 111: 53-64. Available: http://linkinghub. elsevier.com/retrieve/pii/S0165783611002281. Accessed 11 September 2012.
10. R Core Team (2013) R: A Language and Environment for Statistical Computing. Available: http://www.r-project.org/.
11. Grothendieck G (2012) Sqldf: Perform SQL Selects on R Data Frames. Available: http://cran.r-project.org/web/packages/sqldf/index.html.
12. Pante E, Simon-Bouhet B (2013) marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS One 8: e73051. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3760912&tool=pmcentrez&rendertype=abstract. Accessed 21 October 2013.
13. Schnute JT, Boers N, Haigh R, Grandin C, Johnson A, et al. (2013) PBSmapping: Mapping Fisheries Data and Spatial Analysis Tools. Available: http://cran.r-project.org/web/packages/PBSmapping/index.html.
14. Kahle D, Wickham H (2013) Ggmap: A package for spatial visualization with Google Maps and OpenStreetMap. Available: http://cran.r-project.org/web/ packages/ggmap/index.html.
15. EC (2008) Council Regulation (EC) No. 199/2008 concerning the establishment of a Community framework for the collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy. Off J Eur Union L60: 1-12.
16. Marchal P (2008) A comparative analysis of me 'tiers and catch profiles for some French demersal and pelagic fleet. ICES J Mar Sci 65: 674-686.
17. García-Rodríguez M, Fernández ÁM, Esteban A (2006) Characterisation, analysis and catch rates of the small-scale fisheries of the Alicante Gulf (SE Spain) over a 10 years time series. Fish Res 77: 226-238. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0165783605002808. Accessed 15 November 2013.
18. Pelletier D, Ferraris J (2000) A multivariate approach for defining fishing tactics from commercial catch and effort data. Can J Fish Aquat Sci 57: 51-65. Available: http://www.nrcresearchpress.com/doi/abs/10.1139/f99-176.
19. Tzanatos E, Dimitriou E, Katselis G, Georgiadis M, Koutsikopoulos C (2005) Composition, temporal dynamics and regional characteristics of small-scale fisheries in Greece. Fish Res 73: 147-158. Available: http://linkinghub.elsevier.com/retrieve/pii/S0165783604003108. Accessed 15 November 2013.
20. Castro J, Punzón A, Pierce GJ, Marín M, Abad E (2010) Identification of métiers of the Northern Spanish coastal bottom pair trawl fleet by using the partitioning method CLARA. Fish Res 102: 184-190. Available: http://linkinghub.elsevier.com/retrieve/pii/S0165783609003130. Accessed 7 November 2013.
21. Maechler M (2013) cluster: Cluster Analysis Extended Rousseeuw et al. Available: http://cran.r-project.org/web/packages/cluster/index.html.
22. Rousseeuw PJ (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20: 53-65. Available: http://linkinghub.elsevier.com/retrieve/pii/0377042787901257.
23. Bezdek JC (1981) Pattern Recognition with Fuzzy Objective Function Algorithms. Boston, MA: Springer US. Available: http://www.springerlink.com/ index/10.1007/978-1-4757-0450-1.
24. Miyamoto S, Honda K, Ichihashi H (2008) Algorithms for Fuzzy Clustering. Methods in c-Means Clustering with Applications. Kacprzyk J, editor Berlin: Springer-Verlag.
25. Piet GJ, Quirijns FJ, Robinson L, Greenstreet SPR (2007) Potential pressure indicators for fishing, and their data requirements: 110-121.
26. Bourgon R (2013) intervals: Tools for working with points and intervals: 1-35. Available: http://cran.r-project.org/web/packages/interval/index.html.
27. Chang S-K (2011) Application of a vessel monitoring system to advance sustainable fisheries management-Benefits received in Taiwan. Mar Policy 35: 116-121. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0308597X10001491. Accessed 2 December 2013.
28. Fock HO (2011) Natura 2000 and the European Common Fisheries Policy. Mar Policy 35: 181-188. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0308597X10001648. Accessed 15 August 2012.
29. Walker E, Bez N (2010) A pioneer validation of a state-space model of vessel trajectories (VMS) with observers' data. Ecol Modell 221: 2008-2017. Available: http://linkinghub.elsevier.com/retrieve/pii/S0304380010002589. Accessed 14 November 2013.
30. Gerritsen HD, Minto C, Lordan C (2013) How much of the seabed is impacted by mobile fishing gear? Absolute estimates from Vessel Monitoring System (VMS) point data. ICES J Mar Sci 70: 523-531.
31. Chang S-K (2014) Constructing logbook-like statistics for coastal fisheries using coastal surveillance radar and fish market data. Mar Policy 43: 338-346. Available: http://linkinghub.elsevier.com/retrieve/pii/ S0308597X13001450. Accessed 6 December 2013.
32. Campbell MS, Stehfest KM, Votier SC, Hall-Spencer JM (2013) Mapping fisheries for marine spatial planning: Gear-specific vessel monitoring system (VMS), marine conservation and offshore renewable energy. Mar Policy: 1-8. Available: http://linkinghub.elsevier.com/retrieve/pii/S0308597X13002121. Accessed 6 December 2013.
33. Sharples J, Ellis JR, Nolan G, Scott BE (2013) Fishing and the oceanography of a stratified shelf sea. Prog Oceanogr 117: 130-139. Available: http://linkinghub.elsevier.com/retrieve/pii/S007966111300102X. Accessed 6 December 2013.
34. Russo T, Parisi A, Garofalo G, Gristina M, Cataudella S, et al. (2014) SMART: A Spatially Explicit Bio-Economic Model for Assessing and Managing Demersal Fisheries, with an Application to Italian Trawlers in the Strait of Sicily. PLoS One 9: e86222. Available: http://dx.plos.org/10.1371/journal.pone. 0086222. Accessed 24 January 2014.
35. Tsontos VM, Kiefer DA (2003) The Gulf of Maine biogeographical information system project: developing a spatial data management framework in support of OBIS Vers un système d ' information biogéographique sur le Golfe du Maine: mise au point d ' une architecture de gestion de donné. 25: 199-206.
36. Tsontos VM, Kiefer DA (2000) Development of a Dynamic Biogeographic Information System for the Gulf of Maine. Oceanography 13: 25-30. Available: http://www.tos.org/oceanography/archive/13-3-tsontos.html.
37. Bray JC, Curtis J. (1957) An ordination of upland forest communities of southern Wisconsin. Ecol Monogr 27: 325-349.
38. Legendre P, Legendre L (1998) Numerical Ecology. Second. Elsevier Science B.V TN, editor.
39. Ihaka R (2010) R: Lessons Learned, Directions for the Future. Available: https://www.stat.auckland.ac.nz/,ihaka/downloads/JSM-2010.pdf.
40. Kidd S, Frid A, Plater C, editors (2011) The Ecosystem Approach to Marine Planning and Management. Routledge.
41. Scarcella G, Grati F, Raicevich S, Russo T, Gramolini R, et al. (2014) Common sole in the northern and central Adriatic Sea: Spatial management scenarios to rebuild the stock. J Sea Res 89: 12-22. Available: http://linkinghub.elsevier.com/retrieve/pii/S1385110114000264. Accessed 18 April 2014.
42. Russo T, Prestinicola L, Scardi M, Palamara E, Cataudella S, et al. (2010) Progress in modeling quality in aquaculture: an application of the Self-Organizing Map to the study of skeletal anomalies and meristic counts in gilthead seabream (Sparus aurata, L. 1758). J Appl Ichthyol 26: 360-365. Available: http://doi.wiley.com/10.1111/j.1439-0426.2010.01435.x. Accessed 11 September 2012.
43. Russo T, Scardi M, Cataudella S (2014) Applications of Self-Organizing Maps for Ecomorphological Investigations through Early Ontogeny of Fish. PLoS One 9: e86646. Available: http://dx.plos.org/10.1371/journal.pone.0086646. Accessed 24 January 2014.
44. Russo T, Mariani S, Baldi P, Parisi A, Magnifico G, et al. (2009) Progress in modelling herring populations: an individual-based model of growth. ICES JMar Sci 66: 1718-1725. Available: http://icesjms.oxfordjournals.org/cgi/ doi/10.1093/icesjms/fsp204.
45. Russo T, Baldi P, Parisi A, Magnifico G, Mariani S, et al. (2009) Lévy processes and stochastic von Bertalanffy models of growth, with application to fish population analysis. J Theor Biol 258: 521-529. Available: http://linkinghub.elsevier.com/retrieve/pii/S0022519309000290. Accessed 30 July 2012.
46. Lawrence M (2011) CairoDevice: Cairo-based cross-platform antialiased graphics device driver. Available: http://cran.r-project.org/web/packages/ cairoDevice/index.html.
47. James D, Hornik K, Grothendieck G (2013) chron: Chronological objects which can handle dates and times. Available: http://cran.r-project.org/web/ packages/chron/index.html.
48. Rousseeuw P, Struyf A, Hubert M (2013) Package "cluster." Available at: http://cran.r-project.org/web/packages/cluster/index.html.
49. Goslee S, Urban D (2013) Ecodist: Dissimilarity-based functions for ecological analysis. Available: http://cran.r-project.org/web/packages/ecodist/ index.html.
50. Furrer R, Nychka D, Sain S (2013) Fields: Tools for spatial data. Available: http://cran.r-project.org/web/packages/fields/index.html.
51. Verzani J (2012) Gwidgets:gWidgets API for building toolkit-independent, interactive GUIs. Available: http://cran.r-project.org/web/packages/gWidgets/ index.html.
52. Verzani J (2012) Examples for gWidgets Abstract:: 1-40.
53. Fmay MP (2013) Intervals: Weighted Logrank Tests and NPMLE for interval censored data. Available: http://cran.r-project.org/web/packages/interval/index. html.
54. Brownrigg R, Minka TP, Becker RA, Wilks AR (2013) Mapdata: Extra Map Databases. Available: http://cran.r-project.org/web/packages/mapdata/index.html.
55. Brownrigg R, Minka TP, Becker RA, Wilks AR (2013) Maps: Draw Geographical Maps. Available: http://cran.r-project.org/web/packages/maps/index.html.
56. Bivand R (2013) Maptools: Tools for reading and handling spatial objects. Available: http://cran.r-project.org/web/packages/maptools/index.html.
57. Komsta L (2011) Outliers: Tests for outliers. Available: http://cran.r-project.org/web/packages/outliers/index.html.
58. Schnute JT, Boers NM, Haigh R, Couture-beil A (2007) PBS Mapping 2. 54: User ' s Guide User ' s Guide Revised from Canadian Technical Report of Fisheries and Aquatic Sciences 2549.
59. Lemon JB, Bolker B, Oom S, Klein E, Rowlingson B, et al. (2013) Plotrix: Various plotting functions. Available: http://cran.r-project.org/web/packages/ plotrix/index.html.
60. Pebesma E, Bivand R, Rowlingson B, Gomez-Rubio V (2013) Sp: classes and methods for spatial data. Available: http://cran.r-project.org/web/packages/sp/ index.html.