| bold_seq {bold} | R Documentation |
Get sequences for a taxonomic name, id, bin, container, institution, researcher, geographic, place, or gene.
bold_seq(taxon = NULL, ids = NULL, bin = NULL, container = NULL, institutions = NULL, researchers = NULL, geo = NULL, marker = NULL, response = FALSE, ...)
taxon |
(character) Returns all records containing matching taxa. Taxa includes the ranks of phylum, class, order, family, subfamily, genus, and species. |
ids |
(character) Returns all records containing matching IDs. IDs include Sample IDs, Process IDs, Museum IDs and Field IDs. |
bin |
(character) Returns all records contained in matching BINs. A BIN is defined by a Barcode Index Number URI. |
container |
(character) Returns all records contained in matching projects or datasets. Containers include project codes and dataset codes |
institutions |
(character) Returns all records stored in matching institutions. Institutions are the Specimen Storing Site. |
researchers |
(character) Returns all records containing matching researcher names. Researchers include collectors and specimen identifiers. |
geo |
(character) Returns all records collected in matching geographic sites. Geographic sites includes countries and province/states. |
marker |
(character) Returns all records containing matching marker codes. |
response |
(logical) Note that response is the object that returns from the Curl call, useful for debugging, and getting detailed info on the API call. |
... |
Further args passed on to |
A list with each element of length 4 with slots for id, name, gene, and sequence.
http://v4.boldsystems.org/index.php/resources/api?type=webservices
## Not run:
res <- bold_seq(taxon='Coelioxys')
bold_seq(taxon='Aglae')
bold_seq(taxon=c('Coelioxys','Osmia'))
bold_seq(ids='ACRJP618-11')
bold_seq(ids=c('ACRJP618-11','ACRJP619-11'))
bold_seq(bin='BOLD:AAA5125')
bold_seq(container='ACRJP')
bold_seq(researchers='Thibaud Decaens')
bold_seq(geo='Ireland')
bold_seq(geo=c('Ireland','Denmark'))
# Return the http response object for detailed Curl call response details
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$url
res$status_code
res$response_headers
## curl debugging
### You can do many things, including get verbose output on the curl
### call, and set a timeout
bold_seq(taxon='Coelioxys', verbose = TRUE)[1:2]
# bold_seqspec(taxon='Coelioxys', timeout_ms = 10)
## End(Not run)