In ropensci/taxize: Taxonomic Information from Around the Web

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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