Description Usage Arguments Value Author(s) References See Also Examples
View source: R/taxinfo_download.R
Download taxonomic data
1 2 | taxinfo_download(query, fq, fields, verbose = ala_config()$verbose,
use_data_table = TRUE)
|
query |
string: (optional) query of the form field:value (e.g. "genus:Macropus") or a free text search ("Alaba vibex") |
fq |
string: 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
|
verbose |
logical: show additional progress information? [default is set by ala_config()] |
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, or use_data_table is FALSE, then read.table will be used (which may be slower) |
data frame of results, containing one row per taxon, typically with name, guid, and taxonomic information. The columns returned will depend on the field requested
Atlas of Living Australia support@ala.org.au
1 2 3 4 5 6 7 | ## Not run:
# Download data for Fabaceae
x=taxinfo_download("family:Fabaceae",fields=c("guid","parentGuid","kingdom","phylum","class","bioOrder","family","genus","nameComplete"))
## note that requesting "nameComplete" gives the scientific name but requesting "scientificName" will not --- bug to be fixed in ALA's web service
# equivalent direct URL: http://bie.ala.org.au/ws/download?fields=guid,parentGuid,kingdom,phylum,class,bioOrder,family,genus,nameComplete&q=family:Fabaceae
## End(Not run)
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