{ "_id": "6a103b33acfb0bcc41c9b69b", "Package": "algaeClassify", "Title": "Tools to Query the 'Algaebase' Online Database, Standardize\nPhytoplankton Taxonomic Data, and Perform Functional Group\nClassifications", "Version": "2.0.6", "Date": "2026-05-10", "Authors@R": "c(person(\"Vijay\",\"Patil\",email=c(\"vij.patil@gmail.com\"),role=c(\"aut\",\"cre\")),\nperson(\"Torsten\",\"Seltmann\",role=\"aut\"),\nperson(\"Nico\",\"Salmaso\",role=\"aut\"),\nperson(\"Orlane\",\"Anneville\",role=\"aut\"),\nperson(\"Marc\",\"Lajeunesse\",role=\"aut\"),\nperson(\"Dietmar\",\"Straile\",role=\"aut\"))", "Author": "Vijay Patil [aut, cre], Torsten Seltmann [aut], Nico Salmaso\n[aut], Orlane Anneville [aut], Marc Lajeunesse [aut], Dietmar\nStraile [aut]", "Maintainer": "Vijay Patil ", "Description": "Functions that facilitate the use of accepted taxonomic\nnomenclature, collection of functional trait data, and\nassignment of functional group classifications to phytoplankton\nspecies. Possible classifications include Morpho-functional\ngroup (MFG; Salmaso et al. 2015 ) and\nCSR (Reynolds 1988; Functional morphology and the adaptive\nstrategies of phytoplankton. In C.D. Sandgren (ed). Growth and\nreproductive strategies of freshwater phytoplankton, 388-433.\nCambridge University Press, New York). Versions 2.0.0 and later\nincludes new functions for querying the 'algaebase' online\ntaxonomic database (www.algaebase.org), however these functions\nrequire a valid API key that must be acquired from the\n'algaebase' administrators. Note that none of the\n'algaeClassify' authors are affiliated with 'algaebase' in any\nway. Taxonomic names can also be checked against a variety of\ntaxonomic databases using the 'Global Names Resolver' service\nvia its API (). In\naddition, currently accepted and outdated synonyms, and higher\ntaxonomy, can be extracted for lists of species from the 'ITIS'\ndatabase via its JSON web service API. The 'algaeClassify'\npackage is a product of the GEISHA (Global Evaluation of the\nImpacts of Storms on freshwater Habitat and Structure of\nphytoplankton Assemblages), funded by CESAB (Centre for\nSynthesis and Analysis of Biodiversity) and the U.S. Geological\nSurvey John Wesley Powell Center for Synthesis and Analysis,\nwith data and other support provided by members of GLEON\n(Global Lake Ecology Observation Network). DISCLAIMER: This\nsoftware has been approved for release by the U.S. Geological\nSurvey (USGS). Although the software has been subjected to\nrigorous review, the USGS reserves the right to update the\nsoftware as needed pursuant to further analysis and review. No\nwarranty, expressed or implied, is made by the USGS or the U.S.\nGovernment as to the functionality of the software and related\nmaterial nor shall the fact of release constitute any such\nwarranty. Furthermore, the software is released on condition\nthat neither the USGS nor the U.S. Government shall be held\nliable for any damages resulting from its authorized or\nunauthorized use.", "URL": "https://doi.org/10.5066/F7S46Q3F", "License": "CC0", "Encoding": "UTF-8", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 11:44:53 UTC", "User": "root" }, "Config/pak/sysreqs": "libssl-dev", "Repository": "https://vijpatil.r-universe.dev", "Date/Publication": "2026-05-11 08:39:46 UTC", "RemoteUrl": "https://github.com/cran/algaeClassify", "RemoteRef": "HEAD", "RemoteSha": "07f053465d4b4b6005269cd9b3f9eeab63abbefc", "MD5sum": "5dd20969ab85fe269e96833f4389a634", "_user": "vijpatil", "_type": "src", "_file": "algaeClassify_2.0.6.tar.gz", "_fileid": "5bb5cf4f8ff2f9a8c6b76e4e646ac2068988b507e19c708831ae12edc7da9b64", "_filesize": 294021, "_sha256": "5bb5cf4f8ff2f9a8c6b76e4e646ac2068988b507e19c708831ae12edc7da9b64", "_created": "2026-05-11T11:44:53.000Z", "_published": "2026-05-22T11:17:07.866Z", "_distro": "noble", "_jobs": [ { "job": 77368869291, "time": 135, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6917583949" }, { "job": 77368869443, "time": 130, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6917582676" }, { "job": 77368869276, "time": 200, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6917596115" }, { "job": 77368869494, "time": 147, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6917579155" }, { "job": 77368868794, "time": 194, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6917539212" }, { "job": 77368868628, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159196117" }, { "job": 77368868905, "time": 80, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6917566667" }, { "job": 77368869480, "time": 64, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6917561268" }, { "job": 77368869216, "time": 67, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6917561949" } ], "_buildurl": "https://github.com/r-universe/vijpatil/actions/runs/25667956038", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/algaeClassify", "_commit": { "id": "07f053465d4b4b6005269cd9b3f9eeab63abbefc", "author": "Vijay Patil ", "committer": "cran-robot ", "message": "version 2.0.6\n", "time": 1778488786 }, "_maintainer": { "name": "Vijay Patil", "email": "vij.patil@gmail.com", "login": "vijpatil", "uuid": 22459409 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "lubridate", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "methods", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 1 }, { "week": "2025-49", "n": 1 }, { "week": "2026-20", "n": 1 } ], "_tags": [ { "name": "2.0.4", "date": "2025-05-14" }, { "name": "2.0.5", "date": "2025-12-01" }, { "name": "2.0.6", "date": "2026-05-11" } ], "_stars": 8, "_contributors": [ { "user": "vppatil", "count": 6, "uuid": 2015547 }, { "user": "vijpatil", "count": 3, "uuid": 22459409 } ], "_userbio": { "uuid": 22459409, "type": "user", "name": "vijpatil" }, "_downloads": { "count": 252, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/algaeClassify" }, "_mentions": 1, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/algaeClassify.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "vijpatil", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2019-05-20" }, { "version": "1.2.0", "date": "2019-09-14" }, { "version": "1.3.2", "date": "2022-03-12" }, { "version": "2.0.1", "date": "2023-11-22" }, { "version": "2.0.2", "date": "2024-01-12" }, { "version": "2.0.3", "date": "2024-10-11" }, { "version": "2.0.4", "date": "2025-05-14" }, { "version": "2.0.5", "date": "2025-12-01" }, { "version": "2.0.6", "date": "2026-05-11" } ], "_exports": [ "accum", "algaebase_genus_search", "algaebase_output_parse", "algaebase_search_df", "algaebase_species_search", "bestmatch", "date_mat", "genus_search_itis", "genus_species_extract", "get_apikey", "get_apikey_fromfile", "gnr_df", "gnr_simple", "itis_search_df", "mean_naomit", "mfg_csr_convert", "mfg_csr_convert_df", "phyto_ts_aggregate", "sampeff", "set_algaebase_apikey_header", "species_search_itis", "species_to_mfg", "species_to_mfg_df", "traits_to_csr", "traits_to_csr_df", "traits_to_mfg", "traits_to_mfg_df" ], "_datasets": [ { "name": "csrTraits", "title": "Database of functional traits for MFG classification, derived from Rimet et al. 2019", "object": "csrTraits", "class": [ "data.frame" ], "fields": [ "phyto_name", "SAV", "MLD", "MSV", "volume.um3", "surface.area.um2", "Colonial", "Number.of.cells.per.colony", "Geometrical.shape.of.the.colony", "traitCSR", "genus", "species" ], "rows": 1217, "table": true, "tojson": true }, { "name": "lakegeneva", "title": "example dataset from lake Geneva, Switzerland", "object": "lakegeneva", "class": [ "data.frame" ], "fields": [ "biovol_um3_ml", "date_dd_mm_yy", "lake", "month", "phyto_name", "year" ], "rows": 50, "table": true, "tojson": true }, { "name": "mfg_csr_library", "title": "MFG-CSR correspondence based on CSR-trait relationships in Reynolds et al. 1988 and MFG-trait relationships in Salmaso et al. 2015", "object": "mfg_csr_library", "class": [ "data.frame" ], "fields": [ "MFG", "CSR" ], "rows": 33, "table": true, "tojson": true }, { "name": "mfgTraits", "title": "Functional Trait Database derived from Rimet et al.", "object": "mfgTraits", "class": [ "data.frame" ], "fields": [ "phyto_name", "genus", "species", "Mobility.apparatus", "Size", "Colonial", "Filament", "Centric", "Gelatinous", "Aerotopes", "Class", "Order", "MFG.fromtraits" ], "rows": 1113, "table": true, "tojson": true }, { "name": "species_mfg_library", "title": "Trait-based MFG classifications for common Eurasion/North American phytoplankton species. See accompanying manuscript for sources", "object": "species_mfg_library", "class": [ "data.frame" ], "fields": [ "genus", "species", "MFG", "source" ], "rows": 918, "table": true, "tojson": true }, { "name": "traitranges", "title": "surface/volume ratio and max linear dimension criteria for CSR From Reynolds 1988 and Reynolds 2006", "object": "traitranges", "class": [ "data.frame" ], "fields": [ "Measurement", "C.min", "S.min", "R.min", "C.max", "S.max", "R.max", "units", "source" ], "rows": 3, "table": true, "tojson": true } ], "_help": [ { "page": "accum", "title": "Split a dataframe column with binomial name into genus and species columns. Plots change in species richness over time, generates species accumulation curve, and compares SAC against simulated idealized curve assuming all unique taxa have equal probability of being sampled at any point in the time series. (author Dietmar Straile)", "topics": [ "accum" ] }, { "page": "algaebase_genus_search", "title": "Search algaebase for information about a genus of phytoplankton", "topics": [ "algaebase_genus_search" ] }, { "page": "algaebase_output_parse", "title": "Helper function for parsing output from algaebase", "topics": [ "algaebase_output_parse" ] }, { "page": "algaebase_search_df", "title": "Search algaebase for information about a list of phytoplankton names", "topics": [ "algaebase_search_df" ] }, { "page": "algaebase_species_search", "title": "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.", "topics": [ "algaebase_species_search" ] }, { "page": "bestmatch", "title": "fuzzy partial matching between a scientific name and a list of possible matches", "topics": [ "bestmatch" ] }, { "page": "csrTraits", "title": "Database of functional traits for MFG classification, derived from Rimet et al. 2019", "topics": [ "csrTraits" ] }, { "page": "date_mat", "title": "Transform a phytoplankton timeseries into a matrix of abundances for ordination", "topics": [ "date_mat" ] }, { "page": "genus_search_itis", "title": "Wrapper function for several functions in ritis:: Searches ITIS database for matches to a genus name", "topics": [ "genus_search_itis" ] }, { "page": "genus_species_extract", "title": "Split a dataframe column with binomial name into genus and species columns.", "topics": [ "genus_species_extract" ] }, { "page": "get_apikey", "title": "Get value of algaebase API key from Environment variable Return an error if variable not set.", "topics": [ "get_apikey" ] }, { "page": "get_apikey_fromfile", "title": "Get value of algaebase API key from a file", "topics": [ "get_apikey_fromfile" ] }, { "page": "gnr_df", "title": "Wrapper function to apply gnr_simple across a data.frame or list of species names. Modified on 11/18/2025 by Vijay Patil (vpatil@usgs.gov) for algaeClassify v2.0.5 (pending approval on CRAN).", "topics": [ "gnr_df" ] }, { "page": "gnr_simple", "title": "checks species names against a variety of online databases supports fuzzy partial matching, using the Global Names Resolver (https://resolver.globalnames.org/). Modified on 11/18/2025 by Vijay Patil (vpatil@usgs.gov) for algaeClassify v2.0.5 (pending approval on CRAN).", "topics": [ "gnr_simple" ] }, { "page": "itis_search_df", "title": "Wrapper function for applying genus_search_itis and species_search_itis to a whole data.frame containing scientific names", "topics": [ "itis_search_df" ] }, { "page": "lakegeneva", "title": "example dataset from lake Geneva, Switzerland", "topics": [ "lakegeneva" ] }, { "page": "mean_naomit", "title": "Compute mean value while ignoring NA's", "topics": [ "mean_naomit" ] }, { "page": "mfg_csr_convert", "title": "Returns a CSR classification based on Morphofunctional group (MFG). Correspondence based on Salmaso et al. 2015 and Reynolds et al. 1988", "topics": [ "mfg_csr_convert" ] }, { "page": "mfg_csr_convert_df", "title": "Returns a CSR classification based on Morphofunctional group (MFG). Correspondence based on Salmaso et al. 2015 and Reynolds et al. 1988", "topics": [ "mfg_csr_convert_df" ] }, { "page": "mfg_csr_library", "title": "MFG-CSR correspondence based on CSR-trait relationships in Reynolds et al. 1988 and MFG-trait relationships in Salmaso et al. 2015", "topics": [ "mfg_csr_library" ] }, { "page": "mfgTraits", "title": "Functional Trait Database derived from Rimet et al.", "topics": [ "mfgTraits" ] }, { "page": "phyto_ts_aggregate", "title": "Aggregate phytoplankton timeseries based on abundance. Up to 3 grouping variables can be given: e.g. genus, species, stationid, depth range. If no abundance var is given, will aggregate to presence/absence of grouping vars.", "topics": [ "phyto_ts_aggregate" ] }, { "page": "sampeff", "title": "Visually assess change in sampling effort over time (author: Dietmar Straile)", "topics": [ "sampeff" ] }, { "page": "set_algaebase_apikey_header", "title": "Add algaebase API key to curl handle", "topics": [ "set_algaebase_apikey_header" ] }, { "page": "species_mfg_library", "title": "Trait-based MFG classifications for common Eurasion/North American phytoplankton species. See accompanying manuscript for sources", "topics": [ "species_mfg_library" ] }, { "page": "species_search_itis", "title": "Wrapper function for several functions in ritis:: Searches ITIS database for matches to a binomial scientific name outputs matches, current accepted names, synonyms, and higher taxonomy", "topics": [ "species_search_itis" ] }, { "page": "species_to_mfg", "title": "Conversion of a single genus and species name to a single MFG. 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