rfishbase: exploring, manipulating and visualizing FishBase data from R
Abstract
This article introduces a package that provides interactive and programmatic access to the FishBase repository. This package allows interaction with data on over 30 000 fish species in the rich statistical computing environment, R. This direct, scriptable interface to FishBase data enables better discovery and integration essential for large‐scale comparative analyses. This article provides several examples to illustrate how the package works, and how it can be integrated into phylogenetics packages such as ape and geiger.
Citing Literature
Number of times cited according to CrossRef: 74
- Minrui Huang, Liuyong Ding, Jun Wang, Chengzhi Ding, Juan Tao, The impacts of climate change on fish growth: A summary of conducted studies and current knowledge, Ecological Indicators, 10.1016/j.ecolind.2020.106976, 121, (106976), (2021).
- Leonie Färber, Rob van Gemert, Øystein Langangen, Joël M. Durant, Ken H. Andersen, Population variability under stressors is dependent on body mass growth and asymptotic body size, Royal Society Open Science, 10.1098/rsos.192011, 7, 2, (192011), (2020).
- Céline Jézéquel, Pablo A. Tedesco, Rémy Bigorne, Javier A. Maldonado-Ocampo, Hernan Ortega, Max Hidalgo, Koen Martens, Gislene Torrente-Vilara, Jansen Zuanon, Astrid Acosta, Edwin Agudelo, Soraya Barrera Maure, Douglas A. Bastos, Juan Bogotá Gregory, Fernando G. Cabeceira, André L. C. Canto, Fernando M. Carvajal-Vallejos, Lucélia N. Carvalho, Ariana Cella-Ribeiro, Raphaël Covain, Carlos Donascimiento, Carolina R. C. Dória, Cleber Duarte, Efrem J. G. Ferreira, André V. Galuch, Tommaso Giarrizzo, Rafael P. Leitão, John G. Lundberg, Mabel Maldonado, José I. Mojica, Luciano F. A. Montag, Willian M. Ohara, Tiago H. S. Pires, Marc Pouilly, Saúl Prada-Pedreros, Luiz J. de Queiroz, Lucia Rapp Py-Daniel, Frank R. V. Ribeiro, Raúl Ríos Herrera, Jaime Sarmiento, Leandro M. Sousa, Lis F. Stegmann, Jonathan Valdiviezo-Rivera, Francisco Villa, Takayuki Yunoki, Thierry Oberdorff, A database of freshwater fish species of the Amazon Basin, Scientific Data, 10.1038/s41597-020-0436-4, 7, 1, (2020).
- W. Tyler McCraney, Christine E. Thacker, Michael E. Alfaro, Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2020.106862, 151, (106862), (2020).
- Catalina Pimiento, Michael J. Benton, The impact of the Pull of the Recent on extant elasmobranchs, Palaeontology, 10.1111/pala.12478, 63, 3, (369-374), (2020).
- Michael D. Burns, Devin D. Bloom, Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes, Proceedings of the Royal Society B: Biological Sciences, 10.1098/rspb.2019.2615, 287, 1918, (20192615), (2020).
- David M. Anderson, James F. Gillooly, Predicting egg size across temperatures in marine teleost fishes, Fish and Fisheries, 10.1111/faf.12486, 21, 5, (1027-1033), (2020).
- Thomas J. Webb, Aaron Lines, Leigh M. Howarth, Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species, Ecology and Evolution, 10.1002/ece3.6407, 10, 14, (7050-7061), (2020).
- Stéphanie Manel, Pierre-Edouard Guerin, David Mouillot, Simon Blanchet, Laure Velez, Camille Albouy, Loïc Pellissier, Global determinants of freshwater and marine fish genetic diversity, Nature Communications, 10.1038/s41467-020-14409-7, 11, 1, (2020).
- Alexandre C. Siqueira, Renato A. Morais, David R. Bellwood, Peter F. Cowman, Trophic innovations fuel reef fish diversification, Nature Communications, 10.1038/s41467-020-16498-w, 11, 1, (2020).
- Shane A. Blowes, Jonathan M. Chase, Antonio Di Franco, Ori Frid, Nicholas J. Gotelli, Paolo Guidetti, Tiffany M. Knight, Felix May, Daniel J. McGlinn, Fiorenza Micheli, Enric Sala, Jonathan Belmaker, Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance, Journal of Applied Ecology, 10.1111/1365-2664.13549, 57, 3, (578-589), (2020).
- Anh D. Luong, Jo Dewulf, Frederik De Laender, Quantifying the primary biotic resource use by fisheries: A global assessment, Science of The Total Environment, 10.1016/j.scitotenv.2020.137352, 719, (137352), (2020).
- David Griffiths, Foraging habitat determines predator–prey size relationships in marine fishes, Journal of Fish Biology, 10.1111/jfb.14451, 97, 4, (964-973), (2020).
- Friedrich W. Keppeler, Carmen G. Montaña, Kirk O. Winemiller, The relationship between trophic level and body size in fishes depends on functional traits, Ecological Monographs, 10.1002/ecm.1415, 0, 0, (2020).
- Phil J. Bouchet, Tom B. Letessier, Michael Julian Caley, Scott L. Nichol, Jan M. Hemmi, Jessica J. Meeuwig, Submerged Carbonate Banks Aggregate Pelagic Megafauna in Offshore Tropical Australia, Frontiers in Marine Science, 10.3389/fmars.2020.00530, 7, (2020).
- Guillaume Guinot, Lionel Cavin, Distinct Responses of Elasmobranchs and Ray-Finned Fishes to Long-Term Global Change, Frontiers in Ecology and Evolution, 10.3389/fevo.2019.00513, 7, (2020).
- Olivier Larouche, Bailey Benton, Katherine A. Corn, Sarah T. Friedman, Dominique Gross, Mikayla Iwan, Brian Kessler, Christopher M. Martinez, Sierra Rodriguez, Hannah Whelpley, Peter C. Wainwright, Samantha A. Price, Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale, Coral Reefs, 10.1007/s00338-020-01976-w, (2020).
- Samuel R. Borstein, dietr: an R package for calculating fractional trophic levels from quantitative and qualitative diet data, Hydrobiologia, 10.1007/s10750-020-04417-5, (2020).
- Jacqueline A. May, Zeny Feng, Matthew G. Orton, Sarah J. Adamowicz, The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach, Journal of Molecular Evolution, 10.1007/s00239-020-09967-9, (2020).
- Alejandro Trujillo-González, Thane A. Militz, Taxonomically constrained reporting framework limits biodiversity data for aquarium fish imports to Australia, Wildlife Research, 10.1071/WR18135, 46, 4, (355), (2019).
- Frieda Benun Sutton, Anthony B. Wilson, Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes, Evolution, 10.1111/evo.13846, 73, 12, (2451-2460), (2019).
- Rupert A. Collins, Judith Bakker, Owen S. Wangensteen, Ana Z. Soto, Laura Corrigan, David W. Sims, Martin J. Genner, Stefano Mariani, Non‐specific amplification compromises environmental DNA metabarcoding with COI, Methods in Ecology and Evolution, 10.1111/2041-210X.13276, 10, 11, (1985-2001), (2019).
- Kevin Cazelles, Timothy Bartley, Matthew M. Guzzo, Marie‐Hélène Brice, Andrew S. MacDougall, Joseph R. Bennett, Ellen H. Esch, Taku Kadoya, Jocelyn Kelly, Shin‐ichiro Matsuzaki, Karin A. Nilsson, Kevin S. McCann, Homogenization of freshwater lakes: Recent compositional shifts in fish communities are explained by gamefish movement and not climate change, Global Change Biology, 10.1111/gcb.14829, 25, 12, (4222-4233), (2019).
- Colleen M. Petrik, Charles A. Stock, Ken H. Andersen, P. Daniël van Denderen, James R. Watson, Bottom-up drivers of global patterns of demersal, forage, and pelagic fishes, Progress in Oceanography, 10.1016/j.pocean.2019.102124, (102124), (2019).
- Christopher M. Free, James T. Thorson, Malin L. Pinsky, Kiva L. Oken, John Wiedenmann, Olaf P. Jensen, Impacts of historical warming on marine fisheries production, Science, 10.1126/science.aau1758, 363, 6430, (979-983), (2019).
- Arnaud Grüss, Maria L.D. Palomares, Jorrit H. Poelen, Josephine R. Barile, Casey D. Aldemita, Shelumiel R. Ortiz, Nicolas Barrier, Yunne-Jai Shin, James Simons, Daniel Pauly, Building bridges between global information systems on marine organisms and ecosystem models, Ecological Modelling, 10.1016/j.ecolmodel.2019.01.023, 398, (1-19), (2019).
- B. Hayden, M. L. D. Palomares, B. E. Smith, J. H. Poelen, Biological and environmental drivers of trophic ecology in marine fishes - a global perspective, Scientific Reports, 10.1038/s41598-019-47618-2, 9, 1, (2019).
- Maurice Codespoti Goodman, Shawn Michelle Hannah, Benjamin Isaac Ruttenberg, The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes, Journal of Biogeography, 10.1111/jbi.13595, 46, 7, (1438-1450), (2019).
- Catalina Pimiento, Juan L. Cantalapiedra, Kenshu Shimada, Daniel J. Field, Jeroen B. Smaers, Evolutionary pathways toward gigantism in sharks and rays, Evolution, 10.1111/evo.13680, 73, 3, (588-599), (2019).
- Daniel T.I. Bayley, Andrew O.M. Mogg, Andy Purvis, Heather J. Koldewey, Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology, Aquatic Conservation: Marine and Freshwater Ecosystems, 10.1002/aqc.3215, 29, 12, (2026-2044), (2019).
- Katya E. Kovalenko, Lucinda B. Johnson, Valerie J. Brady, Jan J. H. Ciborowski, Matthew J. Cooper, Joseph P. Gathman, Gary A. Lamberti, Ashley H. Moerke, Carl R. Ruetz, Donald G. Uzarski, Hotspots and bright spots in functional and taxonomic fish diversity, Freshwater Science, 10.1086/704713, 38, 3, (480-490), (2019).
- Matt Friedman, Kara L. Feilich, Hermione T. Beckett, Michael E. Alfaro, Brant C. Faircloth, David Černý, Masaki Miya, Thomas J. Near, Richard C. Harrington, A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean, Proceedings of the Royal Society B: Biological Sciences, 10.1098/rspb.2019.1502, 286, 1910, (20191502), (2019).
- Shaw Nozaki Lacy, Derek Corcoran, Dominique Alò, Janeth Lessmann, Francisco Meza, Pablo A. Marquet, Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers, Hydrobiologia, 10.1007/s10750-019-04044-9, (2019).
- Michael E Alfaro, Elizabeth A Karan, Shawn T Schwartz, Allison J Shultz, The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae), Integrative and Comparative Biology, 10.1093/icb/icz119, (2019).
- Arnaud Hélias, Data for Fish Stock Assessment Obtained from the CMSY Algorithm for all Global FAO Datasets, Data, 10.3390/data4020078, 4, 2, (78), (2019).
- Javier Sánchez-Hernández, Taxonomy-based differences in feeding guilds of fish, Current Zoology, 10.1093/cz/zoz015, (2019).
- Nathan Robert Geraldi, G. T. Kellison, Nathan M. Bacheler, Climate Indices, Water Temperature, and Fishing Predict Broad Scale Variation in Fishes on Temperate Reefs, Frontiers in Marine Science, 10.3389/fmars.2019.00030, 6, (2019).
- Jose W. Valdez, Kapil Mandrekar, Assessing the Species in the CARES Preservation Program and the Role of Aquarium Hobbyists in Freshwater Fish Conservation, Fishes, 10.3390/fishes4040049, 4, 4, (49), (2019).
- Patrícia Amorim, Pedro Sousa, Ernesto Jardim, Gui M. Menezes, Sustainability Status of Data-Limited Fisheries: Global Challenges for Snapper and Grouper, Frontiers in Marine Science, 10.3389/fmars.2019.00654, 6, (2019).
- Phoebe A. Woodworth-Jefcoats, Julia L. Blanchard, Jeffrey C. Drazen, Relative Impacts of Simultaneous Stressors on a Pelagic Marine Ecosystem, Frontiers in Marine Science, 10.3389/fmars.2019.00383, 6, (2019).
- Ivan Jarić, Robert J. Lennox, Gregor Kalinkat, Gorčin Cvijanović, Johannes Radinger, Susceptibility of European freshwater fish to climate change: Species profiling based on life‐history and environmental characteristics, Global Change Biology, 10.1111/gcb.14518, 25, 2, (448-458), (2018).
- Elizabeth A. Babcock, Alexander Tewfik, Virginia Burns-Perez, Fish community and single-species indicators provide evidence of unsustainable practices in a multi-gear reef fishery, Fisheries Research, 10.1016/j.fishres.2018.07.003, 208, (70-85), (2018).
- Robert T. Leaf, Megumi C. Oshima, An evaluation of the impacts of alternative food web structure in the northern Gulf of Mexico ecosystem, Ecological Informatics, 10.1016/j.ecoinf.2018.12.005, (2018).
- Christopher D. West, Emilie Hobbs, Simon A. Croft, Jonathan M.H. Green, Sarah Y. Schmidt, Richard Wood, Improving consumption based accounting for global capture fisheries, Journal of Cleaner Production, 10.1016/j.jclepro.2018.11.298, (2018).
- Rob van Gemert, Ken H Andersen, Challenges to fisheries advice and management due to stock recovery, ICES Journal of Marine Science, 10.1093/icesjms/fsy084, 75, 6, (1864-1870), (2018).
- Javier Sánchez‐Hernández, Per‐Arne Amundsen, Ecosystem type shapes trophic position and omnivory in fishes, Fish and Fisheries, 10.1111/faf.12308, 19, 6, (1003-1015), (2018).
- Samuel R. Borstein, James A. Fordyce, Brian C. O’Meara, Peter C. Wainwright, Matthew D. McGee, Reef fish functional traits evolve fastest at trophic extremes, Nature Ecology & Evolution, 10.1038/s41559-018-0725-x, (2018).
- Monique A. Ladds, Nokuthaba Sibanda, Richard Arnold, Matthew R. Dunn, Creating functional groups of marine fish from categorical traits, PeerJ, 10.7717/peerj.5795, 6, (e5795), (2018).
- Philipp Neubauer, James T. Thorson, Michael C. Melnychuk, Richard Methot, Kristan Blackhart, Drivers and rates of stock assessments in the United States, PLOS ONE, 10.1371/journal.pone.0196483, 13, 5, (e0196483), (2018).
- Michael J. Landis, Joshua G. Schraiber, Pulsed evolution shaped modern vertebrate body sizes, Proceedings of the National Academy of Sciences, 10.1073/pnas.1710920114, 114, 50, (13224-13229), (2017).
- Benjamin L. Branoff, Martin Sykes, Quantifying the influence of urban land use on mangrove biology and ecology: A meta‐analysis, Global Ecology and Biogeography, 10.1111/geb.12638, 26, 11, (1339-1356), (2017).
- Matthew R. McCurry, Erich M. G. Fitzgerald, Alistair R. Evans, Justin W. Adams, Colin R. McHenry, Skull shape reflects prey size niche in toothed whales, Biological Journal of the Linnean Society, 10.1093/biolinnean/blx032, 121, 4, (936-946), (2017).
- Benjamin T. Martin, Ron Heintz, Eric M. Danner, Roger M. Nisbet, Integrating lipid storage into general representations of fish energetics, Journal of Animal Ecology, 10.1111/1365-2656.12667, 86, 4, (812-825), (2017).
- Kirsty L. Nash, Reg A. Watson, Benjamin S. Halpern, Elizabeth A. Fulton, Julia L. Blanchard, Improving understanding of the functional diversity of fisheries by exploring the influence of global catch reconstruction, Scientific Reports, 10.1038/s41598-017-10723-1, 7, 1, (2017).
- Luis Artur Valões Bezerra, André Andrian Padial, Filipe Brasil Mariano, Danielle Sequeira Garcez, Jorge Iván Sánchez-Botero, Fish diversity in tidepools: assembling effects of environmental heterogeneity, Environmental Biology of Fishes, 10.1007/s10641-017-0584-3, 100, 5, (551-563), (2017).
- Nicholas K. Dulvy, Holly K. Kindsvater, The Future Species of Anthropocene Seas, Conservation for the Anthropocene Ocean, 10.1016/B978-0-12-805375-1.00003-9, (39-64), (2017).
- Pablo A. Tedesco, Olivier Beauchard, Rémy Bigorne, Simon Blanchet, Laëtitia Buisson, Lorenza Conti, Jean-François Cornu, Murilo S. Dias, Gaël Grenouillet, Bernard Hugueny, Céline Jézéquel, Fabien Leprieur, Sébastien Brosse, Thierry Oberdorff, A global database on freshwater fish species occurrence in drainage basins, Scientific Data, 10.1038/sdata.2017.141, 4, (170141), (2017).
- François Michonneau, Joseph W. Brown, David J. Winter, rotl: an R package to interact with the Open Tree of Life data, Methods in Ecology and Evolution, 10.1111/2041-210X.12593, 7, 12, (1476-1481), (2016).
- Wanderley R. Bastos, José G. Dórea, José Vicente E. Bernardi, Angelo G. Manzatto, Marilia H. Mussy, Leidiane C. Lauthartte, Luiz D. Lacerda, Olaf Malm, Sex-related mercury bioaccumulation in fish from the Madeira River, Amazon, Environmental Research, 10.1016/j.envres.2015.11.001, 144, (73-80), (2016).
- Halley E. Froehlich, Rebecca R. Gentry, Benjamin S. Halpern, Synthesis and comparative analysis of physiological tolerance and life-history growth traits of marine aquaculture species, Aquaculture, 10.1016/j.aquaculture.2016.04.018, 460, (75-82), (2016).
- Jacob Schaefer, Nkrumah Frazier, Jonathan Barr, Dynamics of Near‐Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico, Transactions of the American Fisheries Society, 10.1080/00028487.2015.1111253, 145, 1, (108-119), (2015).
- A. Sagouis, J. Cucherousset, S. Villéger, F. Santoul, S. Boulêtreau, Non‐native species modify the isotopic structure of freshwater fish communities across the globe, Ecography, 10.1111/ecog.01348, 38, 10, (979-985), (2015).
- Rupert A. Collins, Ralf Britz, Lukas Rüber, Phylogenetic systematics of leaffishes (Teleostei: Polycentridae, Nandidae), Journal of Zoological Systematics and Evolutionary Research, 10.1111/jzs.12103, 53, 4, (259-272), (2015).
- Simon Goring, Andria Dawson, Gavin L. Simpson, Karthik Ram, Russ W. Graham, Eric C. Grimm, John W. Williams, neotoma: A Programmatic Interface to the Neotoma Paleoecological Database, Open Quaternary, 10.5334/oq.ab, 1, (2015).
- Wanderley R. Bastos, José G. Dórea, José Vicente E. Bernardi, Leidiane C. Lauthartte, Marilia H. Mussy, Luiz D. Lacerda, Olaf Malm, Mercury in fish of the Madeira river (temporal and spatial assessment), Brazilian Amazon, Environmental Research, 10.1016/j.envres.2015.03.029, 140, (191-197), (2015).
- M. D. McGee, S. R. Borstein, R. Y. Neches, H. H. Buescher, O. Seehausen, P. C. Wainwright, A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids, Science, 10.1126/science.aab0800, 350, 6264, (1077-1079), (2015).
- Tad Dallas, Emily Cornelius, Co-extinction in a host-parasite network: identifying key hosts for network stability, Scientific Reports, 10.1038/srep13185, 5, 1, (2015).
- S. A. Price, T. Claverie, T. J. Near, P. C. Wainwright, Phylogenetic insights into the history and diversification of fishes on reefs, Coral Reefs, 10.1007/s00338-015-1326-7, 34, 4, (997-1009), (2015).
- Rupert Collins, Emanuell Duarte Ribeiro, Valéria Nogueira Machado, Tomas Hrbek, Izeni Farias, A preliminary inventory of the catfishes of the lower Rio Nhamundá, Brazil (Ostariophysi, Siluriformes), Biodiversity Data Journal, 10.3897/BDJ.3.e4162, 3, (e4162), (2015).
- Walter A. Boeger, Flávio M. Marteleto, Letícia Zagonel, Mariana P. Braga, Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America, Zoologica Scripta, 10.1111/zsc.12098, 44, 3, (250-262), (2014).
- S. A. Price, L. Schmitz, C. E. Oufiero, R. I. Eytan, A. Dornburg, W. L. Smith, M. Friedman, T. J. Near, P. C. Wainwright, Two waves of colonization straddling the K–Pg boundary formed the modern reef fish fauna, Proceedings of the Royal Society B: Biological Sciences, 10.1098/rspb.2014.0321, 281, 1783, (20140321), (2014).
- Yakir L. Gagnon, Tracey T. Sutton, Sönke Johnsen, Visual acuity in pelagic fishes and mollusks, Vision Research, 10.1016/j.visres.2013.08.007, 92, (1-9), (2013).
- Shin‐ichiro Oka, Hideyuki Doi, Kei Miyamoto, Nozomi Hanahara, Tetsuya Sado, Masaki Miya, Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation, Environmental DNA, 10.1002/edn3.132, 0, 0, (undefined).
- Daniël Denderen, Henrik Gislason, Joost Heuvel, Ken H. Andersen, Global analysis of fish growth rates shows weaker responses to temperature than metabolic predictions, Global Ecology and Biogeography, 10.1111/geb.13189, 0, 0, (undefined).
