gna_verifier {taxize} | R Documentation |
Verify a list of scientific names against biodiversity data-sources.
Description
This service parses incoming names, executes exact or fuzzy matching as
required, and returns the best-scored result. Optionally, it can also return
matches from data-sources selected by a user.
Usage
gna_verifier(
names,
data_sources = c(1, 12),
all_matches = FALSE,
capitalize = FALSE,
species_group = FALSE,
fuzzy_uninomial = FALSE,
stats = FALSE,
main_taxon_threshold = 0.5,
output_type = "table",
...
)
Arguments
names |
A character vector of taxon names to verify.
|
data_sources |
A character or integer vector with numbers
corresponding to data sources. See the Global Names Architecture
documentation for a list of available options.
|
all_matches |
When TRUE , return all found matches, not only the best
one. Multiple results are returned in results. These results are sorted by
matching quality, the first result is the same as bestResult.
|
capitalize |
When TRUE , capitalize the first letter of a name-string.
|
species_group |
When TRUE , expands the search to species group where
applicable.
|
fuzzy_uninomial |
When TRUE , allows fuzzy matching for uninomial
names.
|
stats |
When TRUE , finds out a kingdom and a taxon (main taxon) that
contain most names. It only takes in account the names matched to the
Catalogue of Life entries. This option is ignored, if the Catalogue of Life
is not included in data-sources.
|
main_taxon_threshold |
A numeric vector from 0.5 to 1. This sets the
minimal percentage for the main taxon discovery.
|
output_type |
A character vector of length 1, either table or
list , indicating the format of the output. The tabular output only
contains values that consistently appear in all results, so list output
can have additional information. For list and json outputs, only values
for unique taxon names are returned, but the table output has rows that
correspond 1-1 with the input data.
|
... |
Curl options passed on to crul::HttpClient
|
Value
Depends on the value of the output_type
option
Author(s)
Zachary S.L. Foster
Examples
## Not run:
gna_verifier(c("Helianthus annuus", "Homo saapiens"))
gna_verifier(c("Helianthus annuus", "Homo saapiens"), all_matches = TRUE)
## End(Not run)
[Package
taxize version 0.10.0
Index]