Function get_taxa()

[peterdesmet]

get_taxa <- function(
    taxon_keys = NULL
    checklist_keys = NULL
    limit = NULL
)

Parameters

If parameter taxon_keys:

• [ ] Allows single taxon key (an integer)
• [ ] Allows vector of taxon keys (vector of integers)
• [ ] Functionality: use functionname_usage() to query e.g. http://api.gbif.org/v1/species/5231190
• [ ] If used together with checklist_keys: assertion error

If parameter checklist_keys:

• [ ] Works with single dataset key (a string)
• [ ] Works with vector of datasets keys (vector of strings)
• [ ] Functionality: use function name_usage(datasetKey = ...)
• [ ] If used together with taxon_keys: assertion error

If parameter limit (e.g. 10)

• [ ] With taxon_keys: limit to 10 taxa
• [ ] With checklist_keys: limit to 10 taxa PER DATASET

Return

• [ ] A dataframe with all returned attributes for any taxa:

key	nubKey	nameKey	taxonID	sourceTaxonKey	kingdom	...
134087746	5567657	15913604	2346	NA	Plantae	...
5567657	5567657	1439808	gbif:5567657	123978664	Plantae	...

• [ ] Columns can be in any order, but key (= input taxonKey) should be first.
• [ ] Don't return metadata such as limit, offset

Warning

• [ ] If taxonKey not found by nameUsage(): store in vector. At end of retrieving all keys, add those to the returned dataframe, with column key populated and all other columns NA. Also provide warning message, listing the keys that were not found at GBIF. Note: this should never happen with parameter checklist_keys. 😄

This function should replace:

• [ ] checklist_import()
• [ ] checklists_import()

Documentation

• [ ] Document all above as succinct as possible with roxygen

[damianooldoni]

with single taxon key (a string) Works with vector of taxon keys (vector of strings)

Are taxon keys character? I always used them as numeric.

[peterdesmet]

You're right. However, taxon keys might come from data file where they are defined as character. But OK, let's force user to cast them to integer before passing to function. I'll update issue body.

[damianooldoni]

As discussed, contrarily to documentation, rgbif allows the usage of key as character. name_usage(key = 1) and name_usage(key = "1") give the same output. Based on this, I will update my get_taxa function as well.

[damianooldoni]

get_taxa is ready for hard testing, @peterdesmet!

[damianooldoni]

I cleaned the branch implement-paging&get-taxa-steps of trias package. Now only get_taxa function is visible. Test directory has also been cleaned up with just tests related to get_taxa function. Package reinstalled and succesfully tested. @peterdesmet: check it please one last time. Thanks!

[peterdesmet]

Will do. Note: always good to add a link to the PR: https://github.com/trias-project/trias/pull/3... but well, it's a bit confusing anyway that we made this issues in this repository rather than trias. 😄

[damianooldoni]

I think we should close this issue because:

1. Function has been implemented, documented and tested. See trias::gbif_get_taxa().
2. We don't use it anymore actually :rofl:

[peterdesmet]

Agreed. If you want to clean up things and remove the function, then you should probably create an issue to do that. 😉