Download taxonomic data

Download taxonomic data

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

Arguments

query	string: (optional) query of the form field:value (e.g. "genus:Heleioporus") 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 ala_fields("general", as_is=TRUE) 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")
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 ala_fields("general", as_is=TRUE) for valid field names. Use fields="all" to include all available fields
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. If this fails, or use_data_table is FALSE, then read.table will be used (which may be slower)

Value

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

References

Associated ALA web service: https://api.ala.org.au/#ws2

See also

ala_fields, ala_config

Examples

if (FALSE) {
## simplest usage
x <- taxinfo_download("rk_genus:Heleioporus")

## Data for Fabaceae with specified fields
x <- taxinfo_download("rk_family:Fabaceae", fields=c("guid", "parentGuid",
"rk_kingdom",
  "rk_phylum", "rk_class", "rk_order", "rk_family", "rk_genus",
  "scientificName"))
}