Check in the scientific name string

Identifies open nomenclature (aff., cf.) in species scientific name, classification under species level (var. and subsp.), and common mistakes in the a species scientific name. It creates a new column with the original string and the new suggested name. It also flags problematic names (character string with numbers, authors, wrong case, or other names besides genus and epithet etc).

Identifies open nomenclature (aff., cf.) in species scientific name, classification under species level (var. and subsp.), and common mistakes in the a species scientific name. It creates a new column with the original string and the new suggested name. It also flags problematic names (character string with numbers, authors, wrong case, or other names besides genus and epithet etc).

check_string(species = NULL, drop_infra = FALSE, flora = TRUE)

check_string(species = NULL, drop_infra = FALSE, flora = TRUE)

Arguments

species	species name in a raw format
drop_infra	Logical. Either to remove any infraspecies classification. Defaults to FALSE
flora	Logical. Either to perform checks specific to plants. Defaults to TRUE

Value

Data frame with `verbatimSpecies` as in the original input, `speciesStatus` with the flags in original data, `species` with a suggestion for a more correct species name, and `remove_author` a boolean column indicating if the original input had author names. See Details for a description of flags in the column `speciesStatus`.

Data frame with `verbatimSpecies` as in the original input, `speciesStatus` with the flags in original data, `species` with a suggestion for a more correct species name, and `remove_author` a boolean column indicating if the original input had author names. See Details for a description of flags in the column `speciesStatus`.

Details

Possible flags returned in `species_status`:

possibly_ok

scientific name following the expected pattern Genus epithet

not_Genus_epithet_format

scientific name not following the expected pattern Genus epithet

variety

species scientific name with variety

subspecies

species scientific name with subspecies

form

species scientific name with form

conferre

open nomenclature cf. in species scientific name

affinis

open nomenclature aff. in species scientific name

group

open nomenclature gr. in species scientific name

name_w_authors

species scientific name has authors

not_name_has_digits

species scientific name has digits, not a valid name

indet

species identified only at genus level

family_as_genus

family as genus, not a valid name

order_as_genus

order as genus, not a valid name

species_nova

species name contains an indication of a new species, possibly not yet a valid name

name_w_non_ascii

species name has non ASCII characters, not a valid name

hybrid_species

hybrid species

not_available

any species entry related to Not Available (NA) status

Possible flags returned in `species_status`:

possibly_ok

scientific name following the expected pattern Genus epithet

not_Genus_epithet_format

scientific name not following the expected pattern Genus epithet

variety

species scientific name with variety

subspecies

species scientific name with subspecies

form

species scientific name with form

conferre

open nomenclature cf. in species scientific name

affinis

open nomenclature aff. in species scientific name

group

open nomenclature gr. in species scientific name

name_w_authors

species scientific name has authors

not_name_has_digits

species scientific name has digits, not a valid name

indet

species identified only at genus level

species_nova

species name contains an indication of a new species, possibly not yet a valid name

name_w_non_ascii

species name has non ASCII characters, not a valid name

not_available

any species entry related to Not Available (NA) status

Flags specific to plants (only if `flora = TRUE`):

hybrid_species

hybrid species

subfamily_as_genus

subfamily as genus, not a valid name

family_as_genus

family as genus, not a valid name

order_as_genus

order as genus, not a valid name

Author

Sara Mortara & Andrea Sánchez-Tapia

Sara Mortara & Andrea Sánchez-Tapia

Examples

check_string("Lindsaea lancea var. falcata")
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>                verbatimSpecies speciesStatus                      species
#> 1 Lindsaea lancea var. falcata       variety Lindsaea lancea var. falcata
#>   remove_author
#> 1          TRUE
check_string(c("Lindsaea lancea var. falcata", "Asplenium Aff. truncorum"))
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>                verbatimSpecies speciesStatus                      species
#> 1 Lindsaea lancea var. falcata       variety Lindsaea lancea var. falcata
#> 2     Asplenium Aff. truncorum       affinis          Asplenium truncorum
#>   remove_author
#> 1          TRUE
#> 2         FALSE
check_string("Asplenium sp.")
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>   verbatimSpecies speciesStatus       species remove_author
#> 1   Asplenium sp.         indet Asplenium sp.         FALSE

check_string("Lindsaea lancea var. falcata")
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>                verbatimSpecies speciesStatus                      species
#> 1 Lindsaea lancea var. falcata       variety Lindsaea lancea var. falcata
#>   remove_author
#> 1          TRUE
check_string(c("Lindsaea lancea var. falcata", "Asplenium Aff. truncorum"))
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>                verbatimSpecies speciesStatus                      species
#> 1 Lindsaea lancea var. falcata       variety Lindsaea lancea var. falcata
#> 2     Asplenium Aff. truncorum       affinis          Asplenium truncorum
#>   remove_author
#> 1          TRUE
#> 2         FALSE
check_string("Asplenium sp.")
#> Warning: argument is not an atomic vector; coercing
#> Warning: argument is not an atomic vector; coercing
#>   verbatimSpecies speciesStatus       species remove_author
#> 1   Asplenium sp.         indet Asplenium sp.         FALSE