algaebase_species_search

Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase.

Functions that facilitate the use of accepted taxonomic nomenclature, collection of
functional trait data, and assignment of functional group classifications to phytoplankton
species. Possible classifications include Morpho-functional group (MFG; Salmaso et al. 2015
<doi:10.1111/fwb.12520>) and CSR (Reynolds 1988; Functional morphology and the
adaptive strategies of phytoplankton. In C.D. Sandgren (ed). Growth and reproductive
strategies of freshwater phytoplankton, 388-433. Cambridge University Press, New York).
Versions 2.0.0 and later includes new functions for querying the
'algaebase' online taxonomic database (www.algaebase.org), however these functions require
a valid API key that must be acquired from the 'algaebase' administrators.
Note that none of the 'algaeClassify' authors are affiliated with 'algaebase' in any way. Taxonomic
names can also be checked against a variety of taxonomic databases using
the 'Global Names Resolver' service via its API (<https://resolver.globalnames.org/api>). In addition,
currently accepted and outdated synonyms, and higher taxonomy, can be extracted for lists of
species from the 'ITIS' database using wrapper functions for the ritis package.
The 'algaeClassify' package is a product of the GEISHA (Global Evaluation of the Impacts of
Storms on freshwater Habitat and Structure of phytoplankton Assemblages), funded by CESAB
(Centre for Synthesis and Analysis of Biodiversity) and the U.S. Geological Survey John Wesley Powell Center for
Synthesis and Analysis, with data and other support provided by members of GLEON
(Global Lake Ecology Observation Network).
DISCLAIMER: This software has been approved for release by the
U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review,
the USGS reserves the right to update the software as needed pursuant to further analysis and
review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the
functionality of the software and related material nor shall the fact of release constitute
any such warranty. Furthermore, the software is released on condition that neither the USGS
nor the U.S. Government shall be held liable for any damages resulting from its authorized
or unauthorized use.

Vijay Patil

algaeClassify

Tools to Query the 'Algaebase' Online Database, Standardize
Phytoplankton Taxonomic Data, and Perform Functional Group
Classifications

Torsten Seltmann

Nico Salmaso

Orlane Anneville

Marc Lajeunesse

Dietmar Straile

algaebase_species_search function

<dl><dt>genus</dt>
<dd>genus name as character string</dd>
<dt>species</dt>
<dd>species name as character string</dd>
<dt>apikey</dt>
<dd>valid key for algaebase API as character string</dd>
<dt>handle</dt>
<dd>curl handle with API key. Will be created if not present.</dd>
<dt>higher</dt>
<dd>boolean should higher taxonomy be included in output?</dd>
<dt>print.full.json</dt>
<dd>boolean returns raw json output if TRUE. Default is FALSE (return R data frame)</dd>
<dt>newest.only</dt>
<dd>boolean should results be limited to the most recent matching entry in algaebase?</dd>
<dt>long</dt>
<dd>boolean return long output including full species name and authorship, and entry date from algaebase.</dd>
<dt>exact.matches.only</dt>
<dd>boolean should results be limited to exact matches?</dd>
<dt>api_file</dt>
<dd>path to text file containing a valid API key</dd></dl>

Arguments

Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase. — algaebase_species_search

<dl>

<dt>genus</dt>
<dd>genus name as character string</dd>


<dt>species</dt>
<dd>species name as character string</dd>


<dt>apikey</dt>
<dd>valid key for algaebase API as character string</dd>


<dt>handle</dt>
<dd>curl handle with API key. Will be created if not present.</dd>


<dt>higher</dt>
<dd>boolean should higher taxonomy be included in output?</dd>


<dt>print.full.json</dt>
<dd>boolean returns raw json output if TRUE. Default is FALSE (return R data frame)</dd>


<dt>newest.only</dt>
<dd>boolean should results be limited to the most recent matching entry in algaebase?</dd>


<dt>long</dt>
<dd>boolean return long output including full species name and authorship, and entry date from algaebase.</dd>


<dt>exact.matches.only</dt>
<dd>boolean should results be limited to exact matches?</dd>


<dt>api_file</dt>
<dd>path to text file containing a valid API key</dd>

</dl>

Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase.

algaebase_species_search: Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase.

Description

Usage

Value

Arguments

Examples