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rfishbase specifications


Unique identifier OMICS_14856
Name rfishbase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.1.2
Stability Stable
methods, utils, testthat, rmarkdown, knitr, tidyr, devtools, R(≥3.0), dplyr(≥0.4.0), lazyeval, httr(≥1.0.0)
Maintained Yes


No version available



  • person_outline Carl Boettiger

Additional information


Publication for rfishbase

rfishbase citations


Shark baselines and the conservation role of remote coral reef ecosystems

Sci Adv
PMCID: 5842041
PMID: 29532033
DOI: 10.1126/sciadv.aaq0333

[…] ther mortality predictors based on life histories and to be robust for low-productive species, such as sharks (). Source life histories were taken from the literature and www.fishbase.org through the rfishbase package (tables S1 and S2). When not available, they were predicted from empirical relationships from other available life histories (hereby, we will use the notation θ^ to indicate a predic […]


Pulsed evolution shaped modern vertebrate body sizes

Proc Natl Acad Sci U S A
PMCID: 5740653
PMID: 29114046
DOI: 10.1073/pnas.1710920114

[…] Standard, fork, and total lengths were extracted from Fishbase, using RFishbase (). For each fish clade, we used an allometric regression to convert all taxa to the most frequently observed length type (). […]


A global database on freshwater fish species occurrence in drainage basins

Sci Data
PMCID: 5625552
PMID: 28972575
DOI: 10.1038/sdata.2017.141

[…] ully checked for typing errors and misspellings. Because taxonomy is a ‘moving target’, species names were standardized based on valid species names and their synonyms reported in FishBase using the ‘rfishbase’ package from the R environment (http://www.R-project.org). For those species names that did not match with any synonym or valid name from FishBase, a manual search was applied in the Catalo […]


Improving understanding of the functional diversity of fisheries by exploring the influence of global catch reconstruction

Sci Rep
PMCID: 5587757
PMID: 28878250
DOI: 10.1038/s41598-017-10723-1

[…] taxa, regardless of taxonomic resolution and thus functional metrics based on the functional groups were estimated using all the catch data. Fine-scale trait data were downloaded from FishBase using rFishBase, . The six traits (habitat, minimum depth, maximum depth, trophic level, maximum length, and body shape) were selected to reflect the role of a species within the ecosystem (Supplementary Ta […]


Signatures of the collapse and incipient recovery of an overexploited marine ecosystem

R Soc Open Sci
PMCID: 5541544
PMID: 28791149
DOI: 10.1098/rsos.170215

[…] is a categorical classification based on the most prevalent prey items (M. Koen-Alonso, Fisheries and Oceans Canada 2014, personal communication). Traits i–iv were obtained from FishBase [] using the rfishbase package in R []. Aggregation (trait v) was obtained through a primary literature search and communication with FishBase (electronic supplementary material, table S2). These functional traits […]


Co extinction in a host parasite network: identifying key hosts for network stability

Sci Rep
PMCID: 4538395
PMID: 26278333
DOI: 10.1038/srep13185

[…] Data on fish traits () were obtained from FishBase [Froese, R. and D. Pauly, www.FishBase.org, accessed 08/2014] a comprehensive fish life history trait database accessible in R using rfishbase, and based on information provided in Lima et al. (2012). The importance of certain fish species in the network may relate to specific host traits. For instance, body size and range size are […]


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rfishbase institution(s)
Center for Population Biology, University of California, Davis, CA, USA; Department of Statistics, University of California, Davis, CA, USA
rfishbase funding source(s)
This work was supported by a Computational Sciences Graduate Fellowship from the U.S. Department of Energy under grant number DE-FG02-97ER25308 and National Science Foundation grant DEB-1061981.

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