Looks up the scientific name of every result in the key in the
GBIF Backbone Taxonomy
and reports names that are misspelled, that are synonyms of a name GBIF
now accepts, or that GBIF does not know. A result written as
"Common name (Genus species)" is checked by the name in parentheses;
other results are checked when they look like a scientific name.
Arguments
- key
A dimoose key.
- kingdom
Optional kingdom ("Plantae", "Animalia", "Fungi", ...), which helps GBIF tell apart names that are used in more than one kingdom.
Value
A data frame with one row per name checked: Taxon (as in the
key), name (the scientific name checked), status ("ok",
"misspelled", "synonym", "not found", or "unchecked" when GBIF
could not be reached), gbif (the name GBIF matched), accepted (the
name GBIF accepts for it), genus, family and order (from GBIF's
classification, used by identifyPhotos()) and note (what to fix, in
words).
Details
This needs an internet connection: one request to GBIF per name, and one more for each synonym.
See also
keyFromSpreadsheet(checkNames = TRUE), which runs this check
and reports problems by spreadsheet row.
Examples
# \donttest{
checkNames(montanaKey(), kingdom = "Plantae")
#> Taxon name status
#> 1 Box elder (Acer negundo) Acer negundo ok
#> 2 Green ash (Fraxinus pennsylvanica) Fraxinus pennsylvanica ok
#> 3 Rocky Mountain maple (Acer glabrum) Acer glabrum ok
#> 4 Bur oak (Quercus macrocarpa) Quercus macrocarpa ok
#> 5 Peachleaf willow (Salix amygdaloides) Salix amygdaloides ok
#> 6 Narrowleaf cottonwood (Populus angustifolia) Populus angustifolia ok
#> 7 Quaking aspen (Populus tremuloides) Populus tremuloides ok
#> 8 Plains cottonwood (Populus deltoides) Populus deltoides ok
#> 9 Black cottonwood (Populus trichocarpa) Populus trichocarpa ok
#> 10 Paper birch (Betula papyrifera) Betula papyrifera ok
#> 11 Water birch (Betula occidentalis) Betula occidentalis ok
#> gbif accepted genus family
#> 1 Acer negundo Acer negundo Acer Sapindaceae
#> 2 Fraxinus pennsylvanica Fraxinus pennsylvanica Fraxinus Oleaceae
#> 3 Acer glabrum Acer glabrum Acer Sapindaceae
#> 4 Quercus macrocarpa Quercus macrocarpa Quercus Fagaceae
#> 5 Salix amygdaloides Salix amygdaloides Salix Salicaceae
#> 6 Populus angustifolia Populus angustifolia Populus Salicaceae
#> 7 Populus tremuloides Populus tremuloides Populus Salicaceae
#> 8 Populus deltoides Populus deltoides Populus Salicaceae
#> 9 Populus trichocarpa Populus trichocarpa Populus Salicaceae
#> 10 Betula papyrifera Betula papyrifera Betula Betulaceae
#> 11 Betula occidentalis Betula occidentalis Betula Betulaceae
#> order note
#> 1 Sapindales
#> 2 Lamiales
#> 3 Sapindales
#> 4 Fagales
#> 5 Malpighiales
#> 6 Malpighiales
#> 7 Malpighiales
#> 8 Malpighiales
#> 9 Malpighiales
#> 10 Fagales
#> 11 Fagales
# }