dot-BIEN_sql function

Run an SQL query on the BIEN database.

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

.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

Returns

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)