Spin up a download request for GBIF occurrence data.
occ_download(..., body = NULL, type = "and", user = NULL, pwd = NULL, email = NULL, curlopts = list()) occ_download_prep(..., body = NULL, type = "and", user = NULL, pwd = NULL, email = NULL, curlopts = list())
... | One or more of query arguments to kick of a download job.
If you use this, don't use |
---|---|
body | if you prefer to pass in the payload yourself, use this parameter. if use this, don't ass anythig to the dots. accepts either an R list, or JSON. JSON is likely easier, since the JSON library jsonlite requires that you unbox strings that shouldn't be auto-converted to arrays, which is a bit tedious for large queries. optional |
type | (charcter) One of equals (=), and (&), or (|), lessThan (<), lessThanOrEquals (<=), greaterThan (>), greaterThanOrEquals (>=), in, within, not (!), like |
user | (character) User name within GBIF's website. Required. See Details. |
pwd | (character) User password within GBIF's website. Required. See Details. |
(character) Email address to recieve download notice done email. Required. See Details. |
|
curlopts | list of named curl options passed on to
|
Argument passed have to be passed as character (e.g.,
'country = US'), with a space between key ('country'), operator ('='),
and value ('US'). See the type
parameter for possible options for
the operator. This character string is parsed internally.
The value can be comma separated, in which case we'll turn that into a
predicate combined with the OR operator, for example,
"taxonKey = 2480946,5229208"
will turn into
'{ "type": "or", "predicates": [ { "type": "equals", "key": "TAXON_KEY", "value": "2480946" }, { "type": "equals", "key": "TAXON_KEY", "value": "5229208" } ] }'
Acceptable arguments to ...
are:
taxonKey = 'TAXON_KEY'
scientificName = 'SCIENTIFIC_NAME'
country = 'COUNTRY'
publishingCountry = 'PUBLISHING_COUNTRY'
hasCoordinate = 'HAS_COORDINATE'
hasGeospatialIssue = 'HAS_GEOSPATIAL_ISSUE'
typeStatus = 'TYPE_STATUS'
recordNumber = 'RECORD_NUMBER'
lastInterpreted = 'LAST_INTERPRETED'
continent = 'CONTINENT'
geometry = 'GEOMETRY'
basisOfRecord = 'BASIS_OF_RECORD'
datasetKey = 'DATASET_KEY'
eventDate = 'EVENT_DATE'
catalogNumber = 'CATALOG_NUMBER'
year = 'YEAR'
month = 'MONTH'
decimalLatitude = 'DECIMAL_LATITUDE'
decimalLongitude = 'DECIMAL_LONGITUDE'
elevation = 'ELEVATION'
depth = 'DEPTH'
institutionCode = 'INSTITUTION_CODE'
collectionCode = 'COLLECTION_CODE'
issue = 'ISSUE'
mediatype = 'MEDIA_TYPE'
recordedBy = 'RECORDED_BY'
see downloads for an overview of GBIF downloads methods
When using the geometry parameter, make sure that your well known text
(WKT) is formatted as GBIF expects it. They expect WKT to have a
counter-clockwise winding order. For example, the following is clockwise
POLYGON((-19.5 34.1, -25.3 68.1, 35.9 68.1, 27.8 34.1, -19.5 34.1))
,
whereas they expect the other order:
POLYGON((-19.5 34.1, 27.8 34.1, 35.9 68.1, -25.3 68.1, -19.5 34.1))
note that coordinate pairs are longitude latitude
, longitude first, then
latitude
you should not get any results if you supply WKT that has clockwise winding order.
also note that occ_search()
/occ_data()
behave differently with
respect to WKT in that you can supply counter-clockwise WKT to those
functions but they treat it as an exclusion, so get all data not
inside the WKT area.
occ_download_prep
: prepares a download request, but DOES NOT execute it.
meant for use with occ_download_queue()
occ_download
: prepares a download request and DOES execute it
For user
, pwd
, and email
parameters, you can set them in one of
three ways:
Set them in your .Rprofile
file with the names gbif_user
,
gbif_pwd
, and gbif_email
Set them in your .Renviron
/.bash_profile
(or similar) file with the
names GBIF_USER
, GBIF_PWD
, and GBIF_EMAIL
Simply pass strings to each of the parameters in the function call
We strongly recommend the second option - storing your details as environment variables as it's the most widely used way to store secrets.
See ?Startup
for help.
GBIF has a limit of 12,000 characters for a download query. This means that you can have a pretty long query, but at some point it may lead to an error on GBIF's side and you'll have to split your query into a few.
See the API docs http://www.gbif.org/developer/occurrence#download for more info, and the predicates docs http://www.gbif.org/developer/occurrence#predicates
# NOT RUN { # occ_download("basisOfRecord = LITERATURE") # occ_download('taxonKey = 3119195') # occ_download('decimalLatitude > 50') # occ_download('elevation >= 9000') # occ_download('decimalLatitude >= 65') # occ_download("country = US") # occ_download("institutionCode = TLMF") # occ_download("catalogNumber = Bird.27847588") # res <- occ_download('taxonKey = 7264332', 'hasCoordinate = TRUE') # pass output directly, or later, to occ_download_meta for more information # occ_download('decimalLatitude > 75') %>% occ_download_meta # Multiple queries # occ_download('decimalLatitude >= 65', 'decimalLatitude <= -65', type="or") # gg <- occ_download('depth = 80', 'taxonKey = 2343454', type="or") # complex example with many predicates # shows example of how to do date ranges for both year and month # res <- occ_download( # "taxonKey = 2480946,5229208", # "basisOfRecord = HUMAN_OBSERVATION,OBSERVATION,MACHINE_OBSERVATION", # "country = US", # "hasCoordinate = true", # "hasGeospatialIssue = false", # "year >= 1999", # "year <= 2011", # "month >= 3", # "month <= 8" # ) # Using body parameter - pass in your own complete query ## as JSON query1 <- '{"creator":"sckott", "notification_address":["myrmecocystus@gmail.com"], "predicate":{"type":"and","predicates":[ {"type":"equals","key":"TAXON_KEY","value":"7264332"}, {"type":"equals","key":"HAS_COORDINATE","value":"TRUE"}]} }' # res <- occ_download(body = query1, curlopts=list(verbose=TRUE)) ## as a list library(jsonlite) query <- list( creator = unbox("sckott"), notification_address = "myrmecocystus@gmail.com", predicate = list( type = unbox("and"), predicates = list( list(type = unbox("equals"), key = unbox("TAXON_KEY"), value = unbox("7264332")), list(type = unbox("equals"), key = unbox("HAS_COORDINATE"), value = unbox("TRUE")) ) ) ) # res <- occ_download(body = query, curlopts = list(verbose = TRUE)) # Prepared query occ_download_prep("basisOfRecord = LITERATURE") # }