Description Usage Arguments Value References See Also Examples
Retrieve NBN occurrence data via the "occurrence download" web service. At least one of taxon
, wkt
, or fq
must be supplied for a valid query. Note that there is a limit of 500000 records per request when using method="indexed"
. Use the method="offline"
for larger requests. For small requests, method="indexed"
likely to be faster.
1 2 3 4 | occurrences(taxon, wkt, fq, fields, extra, qa, method = "indexed", email,
download_reason_id = nbn_config()$download_reason_id, reason,
verbose = nbn_config()$verbose, record_count_only = FALSE,
use_layer_names = TRUE, use_data_table = TRUE)
|
taxon |
string: (optional) query of the form field:value (e.g. "genus:Macropus") or a free text search (e.g. "macropodidae"). Note that
a free-text search is equivalent to specifying the "text" field (i.e. |
wkt |
string: (optional) a WKT (well-known text) string providing a spatial polygon within which to search, e.g. "POLYGON((140 -37,151 -37,151 -26,140.131 -26,140 -37))" |
fq |
string: (optional) 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 |
extra |
string vector: (optional) a vector of field names to include in addition to those specified in |
qa |
string vector: (optional) list of record issues to include in the download. Use |
method |
string: "indexed" (default) or "offline". In "offline" mode, more fields are available and larger datasets can be returned |
email |
string: the email address of the user performing the download (required for |
download_reason_id |
numeric or string: (required unless record_count_only is TRUE) a reason code for the download, either as a numeric ID (currently 0–11) or a string (see |
reason |
string: (optional) user-supplied description of the reason for the download. Providing this information is optional but will help the NBN to better support users by building a better understanding of user communities and their data requests |
verbose |
logical: show additional progress information? [default is set by nbn_config()] |
record_count_only |
logical: if TRUE, return just the count of records that would be downloaded, but don't download them. Note that the record count is always re-retrieved from the NBN, regardless of the caching settings. If a cached copy of this query exists on the local machine, the actual data set size may therefore differ from this record count. |
use_layer_names |
logical: if TRUE, layer names will be used as layer column names in the returned data frame (e.g. "watsonianViceCounties"). Otherwise, layer id value will be used for layer column names (e.g. "cl23") |
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 with an error or warning, or if use_data_table is FALSE, then read.table will be used (which may be slower) |
Data frame of occurrence results, with one row per occurrence record. The columns of the dataframe will depend on the requested fields
Associated NBN web service for record counts: https://api.nbnatlas.org/#ws3
Associated NBN web service for occurence downloads: https://api.nbnatlas.org/#ws4
Field definitions: https://docs.google.com/spreadsheet/ccc?key=0AjNtzhUIIHeNdHhtcFVSM09qZ3c3N3ItUnBBc09TbHc
WKT reference: http://www.geoapi.org/3.0/javadoc/org/opengis/referencing/doc-files/WKT.html
nbn_reasons
for download reasons; nbn_config
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## Not run:
## count of records from this data provider
x <- occurrences(taxon="data_resource_uid:dr356",record_count_only=TRUE)
## download records, with standard fields
x <- occurrences(taxon="data_resource_uid:dr356",download_reason_id=10)
## download records, with all fields
x <- occurrences(taxon="data_resource_uid:dr356",download_reason_id=10,
fields=nbn_fields("occurrence_stored",as_is=TRUE)$name)
## download records, with specified fields
x <- occurrences(taxon="genus:macropus",fields=c("longitude","latitude",
"common_name","taxon_name","Rights"),download_reason_id=10)
## download records in polygon, with no quality assertion information
x <- occurrences(taxon="genus:Sialis",wkt="POLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))",
download_reason_id=10,qa="none",verbose = T)
y <- occurrences(taxon="taxon_name:\"Sialis lutaria\"",fields=c("latitude","longitude","collector"),
download_reason_id=10)
str(y)
# equivalent direct webservice call [see this by setting nbn_config(verbose=TRUE)]:
# https://records-ws.nbnatlas.org/occurrences/index/download?q=taxon_name%
# 3A%22Sialis%20lutaria%22&fields=latitude%2Clongitude%2Cbasis_of_record&
# reasonTypeId=10&sourceTypeId=2001&esc=%5C&sep=%09&file=data
occurrences(taxon="genus:\"Sialis\"",fields=c("latitude","longitude","collector"),
qa="none",fq="collector:Unknown",download_reason_id=10)
# equivalent direct webservice call [see this by setting nbn_config(verbose=TRUE)]:
# https://records-ws.nbnatlas.org/occurrences/index/download?reasonTypeId=10&q=*:*&
# fq=genus:Vulpes&lat=51.5074&lon=0.1278&radius=10.0&qa=none&fields=latitude,longitude&
# reasonTypeId=10&sourceTypeId=2001
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.