Function verify_synonyms()

[peterdesmet]

verify_synonyms <- function(
    taxa = NULL # Dataframe with taxa to verify
    verified_synonyms = NULL # Dataframe with verified synonym info
)

Parameters

taxa: a dataframe with at least the following columns

• [ ] backbone_taxonKey
• [ ] backbone_scientificName
• [ ] backbone_acceptedKey
• [ ] backbone_accepted

verified_synonyms: a dataframe with at least the following columns

• [ ] backbone_taxonKey
• [ ] backbone_scientificName
• [ ] backbone_acceptedKey
• [ ] backbone_accepted
• [ ] backbone_kingdom: to be populated from GBIF (is not in taxa)
• [ ] date_added: to be populated by function
• [ ] verified_key: to be populated manually by expert. Not required by this function, but any other functionality will use this key so it is good to check its existence.
• [ ] remarks: NO CHECK, IS NOT REQUIRED

Functionality (pseudo code):

if in verified_synonyms:
     if taxa.backbone_scientificName != verified_synonyms.backbone_scientificName:
        update in verified_synonyms
        add to updated_scientificName
    if taxa.backbone_accepted != verified_synonyms.backbone_accepted:
        update in verified_synonyms
        add to updated_accepted
    else
        do nothing
else (not in verified_synonyms):
    add to verified_synonyms
    add to new_synonyms

if in verified_synonyms, but not in taxa:
    add to unused_synonyms

Return

• [ ] verified_synonyms: same as input df, but now with updated info. Could be written to file outside the function.
• [ ] new_synonyms: a subset of verified_synonyms (same columns) with synonyms relations that were added (found in taxa, but not in verified_synonyms)
• [ ] unused_synonyms: a subset of verified_synonyms (same columns) with unused synonym relations (found in verified_synonyms, but not in taxa)
• [ ] updated_scientificName: a df with backbone_scientificName + updated_backbone_scientificName
• [ ] updated_accepted: a df with backbone_accepted + updated_backbone_accepted

Documentation

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

[peterdesmet]

This function exists in the trias package and is performing well. Thanks @damianooldoni!