In ropensci/taxize: Taxonomic Information from Around the Web

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2024-12-02

Global Names Verifier is the new version of Global Names Resolver, according to Matthias Grenie.

2024-10-16 (Wednesday October 16)

Working on updating scrapenames. The options have been updated, but it has not been tested.

2024-10-04 (Friday October 4)

It seems some of the functions that use the Global Names APIs no longer work. There seem to be multiple APIs (and corresponding command line tools) with multiple endpoints, so its hard to tell which is the new version for presumably depreciated APIs. I will look into each of the API/tools.

• GNFinder: searches for latin names in text. Seems intended to provide metadata about species mentioned in old publications. Results can be passed to GNVerifier.
• GNVerifier: Used to provide the currently accepted name for a species.

2021-10-13 (Wednesday October 13)

Proposed changes:

• replace data.frames with tibbles for apgFamilies, apgOrders, bold_search, get_*_
• Allow apg_lookup to have multiple inputs/outputs
• Convert camelcase to snake case for apgFamilies, apgOrders (will conflict with corresponding functions), as.* functions, arguments of get_bold
• does dataTypes, includeTree do anything for get_bold?
• should as.* return a taxon_id rather than taxon?
• Put get_*id docs in its own help pages and mark as depreciated in docs
• Add as.bold.taxon_id

2021-10-18 (Monday October 18)

Possible changes:

• All of the get_* and get_*_ functions could be converted into one get_taxa and get_taxa_/get_taxa_data with a db argument. This would allow querying multiple databases at once.
• The get_nbn rec_only examples seem to return the same info. What is supposed to happen?
• When you dont choose when prompted for get_nbn('Poa ann'), you get odd output
• Some of the get_ncbi examples dont work
• get_ncbi "not found" counter not working
• Some of the get_pow examples dont seem to do what they are intended to
• Check get_tps examples
• get_wiki seems to be putting the taxon name in the ID slot for the taxon object, might be intended since name and ID are the same?
• Check get_worms examples
• Make the get_*_ functions return concatenated data frames?
• What is difference between get_*_ functions and *_search functions?
• classification conflicts with taxa::classification
• children and downstream could potentially be the same function with a depth arugument?
• should comm2sci return a taxon object?
• depreciated needs to be updated I think

2021-10-19 (Tuesday October 19)

• tibble in output of eol_dataobjects?

2021-10-20 (Wednesday October 20)

• tibble output for eol_search, eubon_search, fg_name_search, fg_epithet_search, fg_name_by_key, fg_author_search, fg_deprecated_names, gbif_downstream, gbif_parse, gni_details, gni_parse, gni_search, itis_acceptname, itis_downstream, nbn_search, nbn_synonyms, pow_search, pow_lookup, rankagg, sci2comm, synonyms_df, tol_resolve, tpl_families, worms_downstream, vascan_search?
• eol_search: says "A maximum of 30 results", but 50 returned
• eubon_children, eubon_search, and eubon_hierarchy need a better description and perhaps more examples
• The format of fg_all_updated_names is a one column table. Should it be a vector?
• Is the fungorum man page link needed? Other providers do not have a similar one
• Could the result of the intermediate augment of the downstream functions be combined into a single table? I am not sure I really understand the output.
• automate queries greater then 1000 for gbif_downstream, gni_search?
• no examples for gbif_name_usage
• Can genbank2uid be abstracted for other databases where there are IDed entries associated with a taxon (GBIF maybe)?
• More documentation on gni_details would be nice. all_records should take TRUE/FALSE?
• Not all functions have the author field. Should that be added?
• id-accessors has no examples
• id2name, ion could return taxon objects, like the get_* functions. ion could also be integrated into id2name
• what do the *_hierarchy functions do that the downstream and classificaitons functions dont do? are they needed?
• itis_lsid could use some more documentation
• type of output is a tibble for single inputs but a list of tibbles for multiple inputs for itis_native. Probably should be the same for both to help with parsing.
• itis_taxrank return taxon_rank object?
• iucn_getname seems to do a lot of duplicate searches.
• iucn_id does pretty much the same as get_iucn. Is iucn_id needed?
• Are both ncbi_downstream and ncbi_children
• ncbi_get_taxon_summary could be renamed and could return taxon
• the get_* functions could also take taxon IDs as well as names since they return taxon objects.
• Not all functions have a output format in the man pages
• scrapenames examples not working. 404 error
• Save data sets as tibbles: species_plantarum_binomials, theplantlist
• Should status_codes, taxize_capwords be internal?
• Some synonyms, synonyms_df examples not working
• taxize_cite bibtex output would be a nice addition
• tax_name and tax_rank conflict with taxa package. Sam functionality with classification and get_*.
• seems like resolve would be a good generic function but it is defunct
• the tp_* functions were not working when I tested

2021-10-20 (Monday October 20)

Working on making tibble outputs. Stopped after lowest_common

2021-10-26 (Tuesday October 26)

Done with tibble conversion. Working on Fixing tests

Found error with taxa running classification(c('Asteraceae', NA), db = 'itis')

ropensci/taxize documentation built on April 5, 2025, 5:15 a.m.