Description Usage Arguments Value Author(s) References See Also Examples
Retrieve ALA 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 the
current service is limited to a maximum of 500000 records
per request.
1 2 3 4 | occurrences(taxon, wkt, fq, fields, extra, qa,
download_reason_id = ala_config()$download_reason_id, reason,
verbose = ala_config()$verbose, record_count_only = FALSE,
use_layer_names = TRUE, use_data_table = TRUE)
|
taxon |
string: (optional) taxonomic query of the form field:value (e.g. "genus:Macropus") or a free text search ("Alaba vibex") |
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. See
|
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 ALA 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 ala_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 ALA, 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. "radiationLowestPeriodBio22"). Otherwise, layer id value will be used for layer column names (e.g. "el871") |
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
Atlas of Living Australia support@ala.org.au
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
ala_reasons
for download reasons;
ala_config
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | x=occurrences(taxon="data_resource_uid:dr356",record_count_only=TRUE) ## count of records from this data provider
x=occurrences(taxon="data_resource_uid:dr356",download_reason_id=10) ## download records, with standard fields
## Not run:
x=occurrences(taxon="data_resource_uid:dr356",download_reason_id=10,fields=ala_fields("occurrence")$name) ## download records, with all fields
x=occurrences(taxon="macropus",fields=c("longitude","latitude","common_name","taxon_name","el807"),download_reason_id=10) ## download records, with specified fields
x=occurrences(taxon="macropus",wkt="POLYGON((145 -37,150 -37,150 -30,145 -30,145 -37))",download_reason_id=10,qa="none") ## download records in polygon, with no quality assertion information
y=occurrences(taxon="alaba vibex",fields=c("latitude","longitude","el874"),download_reason_id=10)
str(y)
# equivalent direct webservice call: http://biocache.ala.org.au/ws/occurrences/index/download?reasonTypeId=10&q=Alaba%20vibex&fields=latitude,longitude,el874&qa=none
occurrences(taxon="Eucalyptus gunnii",fields=c("latitude","longitude"),qa="none",fq="basis_of_record:LivingSpecimen",download_reason_id=10)
# equivalent direct webservice call: http://biocache.ala.org.au/ws/occurrences/index/download?reasonTypeId=10&q=Eucalyptus%20gunnii&fields=latitude,longitude&qa=none&fq=basis_of_record:LivingSpecimen
## End(Not run)
|
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