dot-BIEN_sql: Run an SQL query on the BIEN database.

In BIEN: Tools for Accessing the Botanical Information and Ecology Network Database

Run an SQL query on the BIEN database.

Description

.BIEN_sql is an internal function used to submit SQL queries.

Usage

.BIEN_sql(
  query,
  view_full_occurrence_individual = NULL,
  agg_traits = NULL,
  species_by_political_division = NULL,
  bien_species_all = NULL,
  ranges = NULL,
  bien_taxonomy = NULL,
  phylogeny = NULL,
  bien_metadata = NULL,
  plot_metadata = NULL,
  analytical_stem = NULL,
  datasource = NULL,
  centroid = NULL,
  limit = NULL,
  return.query = FALSE,
  schema = NULL,
  print.query = FALSE,
  fetch.query = TRUE,
  record_limit = 10000
)

Arguments

query	A PostgreSQL query.
view_full_occurrence_individual	Alternative value to be substituted for "view_full_occurrence_individual" in queries when not NULL.
agg_traits	Alternative value to be substituted for "agg_traits" in queries when not NULL.
species_by_political_division	Alternative value to be substituted for "species_by_political_division" in queries when not NULL.
bien_species_all	Alternative value to be substituted for "bien_species_all" in queries when not NULL.
ranges	Alternative value to be substituted for "ranges" in queries when not NULL.
bien_taxonomy	Alternative value to be substituted for "bien_taxonomy" in queries when not NULL.
phylogeny	Alternative value to be substituted for "phylogeny" in queries when not NULL.
bien_metadata	Alternative value to be substituted for "bien_metadata" in queries when not NULL.
plot_metadata	Alternative value to be substituted for "plot_metadata" in queries when not NULL.
analytical_stem	Alternative value to be substituted for "analytical_stem" in queries when not NULL.
datasource	Alternative value to be substituted for "datasource" in queries when not NULL.
centroid	Alternative value to be substituted for "centroid" in queries when not NULL.
limit	A limit on the number of records to be returned. Should be a single number or NULL (the default).
return.query	Should the query used be returned rather than executed? Default is FALSE
schema	An alternative schema to be accessed. Used for testing purposes.
print.query	Should the query used be printed? Default is FALSE
fetch.query	If TRUE (the default) query is executed using dbFetch. If FALSE, dbGetQuery is used.
record_limit	The number of records to download at once. Defaults to 10000

Value

A dataframe returned by the query.

Note

Using fetch.query = TRUE provides better error handling, but fetch.query = FALSE results in a more useful (but uncatchable) error.

Examples

## Not run: 
.BIEN_sql("SELECT DISTINCT country, scrubbed_species_binomial FROM view_full_occurrence_individual 
WHERE country in ( 'United States' );")
## End(Not run)

BIEN documentation built on April 3, 2025, 9:22 p.m.