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log.Rmd
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---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
# Date:
clipr::write_clip(paste0('## ', format(Sys.time(), "%F (%A %B %e)\n\n")))
# Date and time:
clipr::write_clip(paste0('## ', format(Sys.time(), "%F %X %Z (%A %B %e)\n\n")))
```
## 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')`