Note for occurrence fields: only fields that are indexed in the ALA
database can be queried (e.g. used in the fq
parameter in
occurrences
. These fields are identified by the indexed
column in ala_fields("occurrence")
. Only fields that are stored in
the database can be returned as part of an occurrences
call. These
fields are identified by the stored
column in
ala_fields("occurrence")
. The calling syntaxes
ala_fields("occurrence_stored")
and
ala_fields("occurrence_indexed")
are for convenience, and are
equivalent to subset(ala_fields("occurrence"),stored)
and
subset(ala_fields("occurrence"),indexed)
.
ala_fields(fields_type = "occurrence", as_is = TRUE)field_info(field_id, maxrows = 50, record_count_only = FALSE)
text: one of the following
"general" - for searching taxa, datasets, layers, and collections metadata
"occurrence" - for species occurrence records
"occurrence_stored" - can be returned as part of a species occurrence
record search (equivalent to subset(ala_fields("occurrences"),stored)
)
"occurrence_indexed" - can be queried as part of a species occurrence
record search (equivalent to
subset(ala_fields("occurrences"),indexed)
)
"layers" - fields associated with the environmental and contextual
layers. For additional information
on layers, including metadata and licensing, see search_layers
"assertions" - potential issues flagged on one or more occurrence record fields
"images - for image search
logical: if TRUE, leave the field names as they are returned
from the ALA web services. Arguments that are passed directly to the ALA's
web services (e.g. parameter fq
in occurrences
) should
use field names in this format. If as_is
is FALSE, the returned
$names entries will be modified to make them consistent with the
corresponding column names in R data.frames returned by e.g.
occurrences
. as_is = FALSE
has no effect when
fields_type
is "layers". Note that prior to v1.20,
as_is = FALSE
did not work correctly.
text: id of environmental/contextual layer field for which to look up information Prepend "el" for "environmental" (gridded) layers and "cl" for "contextual" (polygonal) layers
integer: maximum number of records to download. Some
contextual layers (those with field_id
s starting with "cl") have a
very large number of records and attempting to download the full set can
cause R to crash. Specifying -1 for maxrows will download the full set of
records for that field
logical: if TRUE, return just the count of records that would be downloaded, but don't download them. This really only makes sense for contextual layers, because environmental layers have only one record per layer
If record_count_only
is TRUE, the number of records is
returned as numeric. Otherwise, a data frame containing the field name and
various attributes; an empty data frame is returned if no match is found
Relevant ALA web services:
for fields_type "occurrence": https://api.ala.org.au/#ws72
for fields_type "general": https://api.ala.org.au/#ws88
for fields_type "layers": https://api.ala.org.au/#ws11 (see also descriptions of the spatial layers: https://spatial.ala.org.au/ws/layers/index)
for fields_type "assertions": https://api.ala.org.au/#ws81
search_layers
to search for spatial layers
# NOT RUN {
l <- ala_fields("layers")
l[, 4]
o <- ala_fields("occurrence")
o[1:13, ]
a <- ala_fields("assertions")
a$description
field_info("cl22")
field_info("el767")
# }
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