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rfishbase: exploring, manipulating and visualizing FishBase data from R.

C Boettiger1, D T Lang, P C Wainwright

  • 1Center for Population Biology, University of California, Davis, CA 95616, USA. cboettig@ucdavis.edu

Journal of Fish Biology
|November 8, 2012
PubMed
Summary
This summary is machine-generated.

A new R package offers direct access to FishBase, enabling interactive exploration of data for over 30,000 fish species. This facilitates large-scale comparative analyses and integration with phylogenetic tools.

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Area of Science:

  • Ichthyology
  • Bioinformatics
  • Computational Biology

Background:

  • FishBase is a comprehensive global information system on fish species.
  • Accessing and integrating FishBase data for large-scale analyses can be challenging.
  • The R statistical environment is widely used in ecological and evolutionary research.

Purpose of the Study:

  • To introduce a new R package for interactive and programmatic access to the FishBase repository.
  • To enable efficient discovery and integration of FishBase data within R.
  • To demonstrate the utility of the package for comparative analyses and phylogenetic studies.

Main Methods:

  • Development of an R package providing a direct interface to FishBase.
  • Illustrative examples showcasing package functionality.
  • Integration examples with existing R packages like 'ape' and 'geiger'.

Main Results:

  • The package allows seamless interaction with data for over 30,000 fish species.
  • Direct, scriptable access to FishBase data is achieved.
  • The package facilitates integration with phylogenetic analysis workflows.

Conclusions:

  • The R package enhances the usability of FishBase data for researchers.
  • It supports advanced comparative and phylogenetic analyses in ichthyology and related fields.
  • This tool promotes more efficient data-driven scientific discovery.