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vijaybarve / taxotools

Tools to Handle Taxonomic Lists
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Create species level entries for nominal subspecies in synonymize_subspecies #86

Open vijaybarve opened 3 years ago

vijaybarve commented 3 years ago

In case species level entry is missing, create that from nominal subspecies in synonymize_subspecies

Jegelewicz commented 3 years ago

Please do not just create things! Rather throw a list of these issues for review.

Let's assume that Amphipsylla phaiomydis phaiomydis was in the file as Amphipsyla phaiomydis phaiomydis. The misspelled species name would then get added to the file to please the synonymy, when really, the spelling should be corrected.

vijaybarve commented 3 years ago

Maybe a parameter like: "generate_missing_nominate" = True/False If I were to try to explain: Setting this to True will generate a nominate species record in the output of 'synonymize_subspecies' in cases where it is inferred to exist based on subspecies names, but was not found in the input list of names. This is useful if some or all names are recorded at the infraspecific level. WARNING: this has the potential to generate invalid names (e.g., if the nominate species is not missing, but rather misspelled in the stem of the subspecies name). @njdowdy

vijaybarve commented 3 years ago

Maybe you can create an additional binary-valued column that tells the user if it was an row that existed in the input of synonymize_subspecies or if it was a row that was generated by taxotools (and so may require manual review). @njdowdy