Description Usage Arguments Value References See Also Examples
Download taxonomic data
1 2 | taxinfo_download(query, fq, fields, verbose = nbn_config()$verbose,
use_data_table = TRUE)
|
query |
string: (optional) query of the form field:value (e.g. "genus:Macropus") or a free text search ("Alaba vibex") |
fq |
string: character string or vector of strings, specifying filters to be applied to the original query.
These are of the form "INDEXEDFIELD:VALUE" e.g. "kingdom:Fungi". See |
fields |
string vector: (optional) a vector of field names to return. Note that the columns of the returned data
frame are not guaranteed to retain the ordering of the field names given here. If not specified, a default list of
fields will be returned. See |
verbose |
logical: show additional progress information? [default is set by nbn_config()] |
use_data_table |
logical: if TRUE, attempt to read the data.csv file using the fread function from the data.table package. Requires data.table to be available. If this fails, or use_data_table is FALSE, then read.table will be used (which may be slower) |
data frame of results, containing one row per taxon, typically with name, guid, and taxonomic information. The columns returned will depend on the field requested
Associated NBN web service: https://api.nbnatlas.org/#ws2
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
## simplest usage
x <- taxinfo_download("rk_genus:Macropus")
## Data for Fabaceae with specified fields
x <- taxinfo_download("rk_family:Fabaceae",fields=c("guid","parentGuid","rk_kingdom","rk_phylum",
"rk_class","rk_order","rk_family","rk_genus","scientificName"))
# equivalent direct URL: https://species-ws.nbnatlas.org/download?q=rk_family%3AFabaceae&fields=
# guid%2CparentGuid%2Crk_kingdom%2Crk_phylum%2Crk_class%2Crk_order%2Crk_family%2Crk_genus%
# 2CscientificName
## End(Not run)
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