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ropensci / taxa

taxonomic classes for R
https://docs.ropensci.org/taxa
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For fuzzy matching of taxon names, report name changes #137

Closed zachary-foster closed 6 years ago

zachary-foster commented 6 years ago

Something like

obj <- taxa::extract_tax_data(names(seqs), regex = '^([a-zA-Z_ -.]+)_(NCBI|F|V)$',
                              key = c(orig_name = "fuzzy_name", source = "info"))
##  Peronospora_schactaii --> Peronospora schachtii
##  Peronospora_sp --> Peronospora
##  Peronosppora_destructor --> Peronospora destructor
##  Phytophthora_asiatiacae --> Phytophthora asiatica
##  Phytophthora_cf_citricola --> Phytophthora citricola
##  Phytophthora_cf_citrophthora --> Phytophthora citrophthora
##  Phytophthora_cf_cryptogea --> Phytophthora cryptogea
##  Phytophthora_cf_heveae --> Phytophthora heveae
...