Tools to Query the 'Algaebase' Online Database, Standardize Phytoplankton Taxonomic Data, and Perform Functional Group Classifications
Split a dataframe column with binomial name into genus and species col...
Search algaebase for information about a genus of phytoplankton
Helper function for parsing output from algaebase
Search algaebase for information about a list of phytoplankton names
Retrieve taxonomic information from the algaebase online database (www...
fuzzy partial matching between a scientific name and a list of possibl...
Transform a phytoplankton timeseries into a matrix of abundances for o...
Wrapper function for several functions in ritis:: Searches ITIS databa...
Split a dataframe column with binomial name into genus and species col...
Get value of algaebase API key from a file
Get value of algaebase API key from Environment variable Return an err...
Wrapper function to apply gnr_simple across a data.frame or list of sp...
checks species names against a variety of online databases supports fu...
Wrapper function for applying genus_search_itis and species_search_iti...
Compute mean value while ignoring NA's
Returns a CSR classification based on Morphofunctional group (MFG). Co...
Returns a CSR classification based on Morphofunctional group (MFG). Co...
Aggregate phytoplankton timeseries based on abundance. Up to 3 groupin...
Visually assess change in sampling effort over time (author: Dietmar S...
Add algaebase API key to curl handle
Wrapper function for several functions in ritis:: Searches ITIS databa...
Wrapper function to apply species_phyto_convert() across a data.frame
Conversion of a single genus and species name to a single MFG. Uses sp...
Add CSR functional group classifications to a dataframe of phytoplankt...
Assign phytoplankton species to CSR functional groups, based on surfac...
Assign morphofunctional groups to a dataframe of functional traits and...
Assign MFG based on binary functional traits and taxonomy (Class and O...
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.