algaeClassify
Tools to Query the 'Algaebase' Online Database, Standardize Phytoplankton Taxonomic Data, and Perform Functional Group Classifications
Description
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 In addition, currently accepted and outdated synonyms, and higher taxonomy, can be extracted for lists of species from the 'ITIS' database using wrapper functions for the ritis package.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.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | ERROR |
| r-devel-linux-x86_64-fedora-gcc | ERROR |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | ERROR |
| r-patched-linux-x86_64 | ERROR |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | ERROR |
Check details (6 non-OK)
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
examples
Running examples in 'algaeClassify-Ex.R' failed
The error most likely occurred in:
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
examples
Running examples in 'algaeClassify-Ex.R' failed
The error most likely occurred in:
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ### database for matches to a genus name
> ### Aliases: genus_search_itis
>
> ### ** Examples
>
> genus='Anabaena'
> genus_search_itis(genus,higher=FALSE)
Error: lexical error: invalid char in json text.
<html><head></head><body><p>Que
(right here) ------^
Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 23, 2026
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
>
...[truncated]...
FALSE)
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) :
Failure when receiving data from the peer [services.itis.gov]:
Recv failure: Connection reset by peer
Calls: genus_search_itis -> tryCatch -> tryCatchList
Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 20, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 19, 2026
examples
Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gnr_df
> ### Title: Wrapper function to apply gnr_simple across a data.frame or list
> ### of
...[truncated]...
lagioselmis+nannoplanctica%7CMonoraphidium+convolutum%7 [... truncated]
Error in gnr_df(lakegeneva, "genus_species") :
No matches or too many requests. Wait several minutes and retry your search, or select a different data source.
Execution halted