Names provided in a character vector will be compared with names stored in
slot taxonNames within an object of class taxlist by
using the function stringdist::stringsim().
Usage
match_names(x, object, ...)
# S4 method for class 'character,character'
match_names(
x,
object,
UsageID,
best = 1,
nomatch = TRUE,
method = "lcs",
cutlevel = NULL,
...
)
# S4 method for class 'character,missing'
match_names(x, best, cutlevel, nomatch = TRUE, ...)
# S4 method for class 'character,taxlist'
match_names(
x,
object,
show_concepts = FALSE,
accepted_only = FALSE,
include_author = FALSE,
...
)Arguments
- x
A character vector with names to be compared.
- object
Either a character vector or a taxlist object containing the taxonomic list for comparison. If missing, the similarity of each name in 'x' will be compared with the rest of the names in the same vector.
- ...
Further arguments passed among methods.
- UsageID
A vector with IDs for single usage names in the compared list. If the IDs are duplicated or not as much as names in 'object', the function retrieves an error message. If missing, this function will number every name anew (see column 'TaxonUsageID' in the output object).
- best
Integer value indicating how many matches should be displayed in the output. Matches with the same value of similarity will be considered as one. Note that this argument will be overrode by 'cutlevel'.
- nomatch
A logical value indicating wheter names without matches should be included in the output (
'nomatch = TRUE') or not ('nomatch = FALSE').- method
Further arguments passed to
stringdist::stringsim().- cutlevel
A numeric value indicating a cut level of similarity, considering as match names with similarities equal or bigger than the cut value. This argument overrides 'best'.
- show_concepts
Logical value indicating whether the respective taxon concepts should be displayed in output or not.
- accepted_only
Logical value indicating whether only accepted names should be matched or all usage names (including synonyms).
A logical value indicating whether the author name in object (method for taxlist) should be included in the matching list or not.
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Names to be compared
species <- c("Cyperus papyrus", "Typha australis", "Luke Skywalker")
## Comparing character vectors
match_names(c("Cyperus paper", "TIE fighter"), species)
#> idx submittedname TaxonUsageID TaxonName match similarity
#> 1 1 Cyperus paper 1 Cyperus papyrus 1 0.8571429
#> 2 2 TIE fighter 2 Typha australis 1 0.3076923
## Retrieve taxon usage names
match_names(species, Easplist)
#> idx submittedname TaxonUsageID TaxonName
#> 1 1 Cyperus papyrus 206 Cyperus papyrus
#> 2 2 Typha australis 51999 Typha australis
#> 3 3 Luke Skywalker 51565 Loudetia kagerensis
#> AuthorName match similarity
#> 1 L. 1 1.0000000
#> 2 Schumach. 1 1.0000000
#> 3 (K. Schum.) C.E. Hubb. ex Hutch. 1 0.4848485
## Display accepted names in output
match_names(x = species, object = Easplist, show_concepts = TRUE)
#> idx submittedname TaxonUsageID TaxonName
#> 1 1 Cyperus papyrus 206 Cyperus papyrus
#> 2 2 Typha australis 51999 Typha australis
#> 3 3 Luke Skywalker 51565 Loudetia kagerensis
#> AuthorName match similarity TaxonConceptID
#> 1 L. 1 1.0000000 206
#> 2 Schumach. 1 1.0000000 50105
#> 3 (K. Schum.) C.E. Hubb. ex Hutch. 1 0.4848485 51565
#> AcceptedTaxonName AcceptedAuthorName Level
#> 1 Cyperus papyrus L. species
#> 2 Typha domingensis Pers. species
#> 3 Loudetia kagerensis (K. Schum.) C.E. Hubb. ex Hutch. species
# Using cut value for similarity
match_names(x = species, object = Easplist, cutlevel = 0.8)
#> idx submittedname TaxonUsageID TaxonName AuthorName match similarity
#> 1 1 Cyperus papyrus 206 Cyperus papyrus L. 1 1.0000000
#> 2 2 Typha australis 51999 Typha australis Schumach. 1 1.0000000
#> 3 2 Typha australis 53125 Typha aequalis Schnizl. 2 0.8275862
#> 4 3 Luke Skywalker NA <NA> <NA> 0 NA