taxinfo_download {ALA4R}R Documentation

Download taxonomic data


Download taxonomic data


taxinfo_download(query, fq, fields, verbose = ala_config()$verbose,
  use_data_table = TRUE)



string: (optional) query of the form field:value (e.g. "genus:Macropus") or a free text search ("Alaba vibex")


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 ala_fields("general") for all the fields that are queryable. NOTE that fq matches are case-sensitive, but sometimes the entries in the fields are not consistent in terms of case (e.g. kingdom names "Fungi" and "Plantae" but "ANIMALIA"). fq matches are ANDed by default (e.g. c("field1:abc","field2:def") will match records that have field1 value "abc" and field2 value "def"). To obtain OR behaviour, use the form c("field1:abc OR field2:def")


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 ala_fields("general") for valid field names


logical: show additional progress information? [default is set by ala_config()]


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


See Also

ala_fields, ala_config


## Not run: 
# Download data for Fabaceae
## 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:,parentGuid,kingdom,phylum,class,bioOrder,family,genus,nameComplete&q=family:Fabaceae

## End(Not run)

[Package ALA4R version 1.01 Index]