Reclassify ITIS species based off a list of higher taxonomic groupings

itis_reclassify(tsn, categories, uncategorized_name = "Uncategorized")

Arguments

tsn

A vector of Taxonomic Serial Numbers to be evaluated.

categories

A list of the categories and associated TSN values. within a list of a category, a minus (-) in front of a number is short hand to remove organisms within that tsn's taxonomy from being listed in a category. See the example for an instance where that makes sense.

uncategorized_name

A string of what to call the missing value.

Value

df_out, tsn_indata

Examples

itis_reclassify(tsn = c(83677, # subphylum Crustacea; shellfish 172746, # Scophthalmus aquosus; finfish 173747, # class Reptilia; uncategorized as part of tetrapoda 98678), # Cancer borealis; shellfish categories = list('Finfish' = c(914179, # Infraphylum Gnathostomata -914181), # Tetrapoda; - = do NOT include "Shellfish" = c(82696, # Phylum Arthropoda 69458)), # Phylum Mollusca uncategorized_name = "uncategorized")
#> $df_out #> TSN category valid rank sciname #> 1 172746 Finfish valid species Scophthalmus aquosus #> 2 83677 Shellfish valid subphylum Crustacea #> 3 98678 Shellfish valid species Cancer borealis #> 4 173747 uncategorized valid class Reptilia #> #> $tsn_indata #> $`173747` #> name rank id #> 1 Animalia kingdom 202423 #> 2 Bilateria subkingdom 914154 #> 3 Deuterostomia infrakingdom 914156 #> 4 Chordata phylum 158852 #> 5 Vertebrata subphylum 331030 #> 6 Gnathostomata infraphylum 914179 #> 7 Tetrapoda superclass 914181 #> 8 Reptilia class 173747 #> #> attr(,"class") #> [1] "classification" #> attr(,"db") #> [1] "itis" #>