worms v0.2.1

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by Jan Holstein

Retriving Aphia Information from World Register of Marine Species

Retrieves taxonomic information from <http://www.marinespecies.org> using WoRMS' RESTful Webservice. Utility functions aim at taxonomic consistency.

Readme

worms

Retriving Aphia Information from World Register of Marine Species (www.marinespecies.org) using WoRMS´ RESTful Webservice

Build a consistent and WoRMS complient taxonomic dataset. Add the respective valid taxa to your taxonimic dataset. For your taxa, add the respective valid taxa to your taxonimic dataset. For your taxa, get the Aphia ID of the currently accepted taxon, which is not neccessarily identical to the valid Aphia id provided by WoRMS (AFAIunderstood in case of deleted or resurrected taxa).


Installation

Just issue

devtools::install_github("janhoo/worms")

You may need to (install.packages("devtools")) first.

Done.

Usage

issue library(worms),
use the package documentation, e.g.,
type ?worms and check the index to read function

Contributing

  1. Fork it!
  2. Create your feature branch: git checkout -b my-new-feature
  3. Commit your changes: git commit -am 'Add some feature'
  4. Push to the branch: git push origin my-new-feature
  5. Submit a pull request :D

Contact


License

This code is licensed to you under the terms of the GNU AFFERO GENERAL PUBLIC LICENSE version 3.0 or higher.


Version History

0.2.1 better documentation, verbose behavior

  • WoRMS copyright information and proper citation
  • removed 7 non-ASCII containing entries from data(northseamacrozoobenthos)
  • some code hardening

0.2.0 implements new methods and data

  • search by id (wormsbyid)
  • fuzzy matching (wormsbymatchnames)
  • based on dataset, add taxa to represent every taxon with the respective accepted taxa (if possible)
  • add reference to the current accepted species (must not be valid AphiaID)
  • wormsbynames now can do fuzzy maching as well
  • fixes issue where deleted or resurrected entries are preferred
  • fixes issue where a single non-empty result returned will break the code

Todo / Known Bugs

  • proper error handling
  • wormsconsolidate does not properly communicates only partial successful operations
  • wormsbynames: better rules for deciding which entry to take
  • a basic function or switch in wormsbynames() that retrieves all entries for a given name

0.1.0 retrieves WoRMS Aphia information and turns them into a data.frame


Versioning Semantics

Releases will be numbered with the following semantic versioning format: major.minor.patch

And constructed with the following guidelines:

  • Breaking backward compatibility bumps the major (resets minor and patch)
  • New additions without breaking backward compatibility bumps the minor (resets patch)
  • Bug fixes and misc changes bumps the patch

Functions in worms

Name Description
wormsconsolidate Recursivly retrieves respective "accepted" AphiaRecords for all synonyms if not already there
wormsaccepted Constructs "accepted_id" column which contains the "AphiaID" of the respective "accepted" taxon
wormsbyid GET AphiaRecordByAphiaID
wormsbymatchnames GET AphiaRecordsByMatchNames
wormsbynames GET AphiaRecordsByNames
northseamacrozoobenthos Over 1600 taxonomic, vernacular and trivial names of benthic critters from the North Sea
worms worms: Use WoRMS RESTful webservice to scrape Aphia information from World Register of Marine Species
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Details

Type Package
License GNU Affero General Public License
Encoding UTF-8
LazyData true
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-06-18 14:17:05 UTC; holstein
Repository CRAN
Date/Publication 2017-06-18 14:52:07 UTC
depends httr , plyr
Contributors

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