queryCDM: Query the Common Data Model with Annotations
In patelm9/chariot: chariot Package

Description Usage Arguments Value See Also Examples

Query a Common Data Model table with automatic joins with any Concept Id to the Concept table with the appropriate prefix.

queryCDM(
  sql_statement,
  write_schema = "patelm9",
  vocab_schema = "omop_vocabulary",
  conn,
  conn_fun = "connectAthena()",
  skip_cache = FALSE,
  override_cache = FALSE,
  cache_only = FALSE,
  cache_resultset = TRUE,
  render_sql = TRUE,
  render_only = FALSE,
  verbose = TRUE,
  sleepTime = 1
)

`sql_statement`	SQL query
`write_schema`	Schema to write the staged data to for a join to Concept table.
`vocab_schema`	Schema where to Concept table can be found.
`conn`	Connection object. If provided, diverts queries to the connection instead of the local Athena instance without caching features.
`skip_cache`	Skip the caching altogether and directly query the database.
`override_cache`	If TRUE, the cache will not be loaded and will be overwritten by a new query. For override_cache to take effect, skip_cache should be FALSE.
`cache_only`	Loads from the cache and does not query the database. A NULL object is returned if a resultset was not cached.
`cache_resultset`	(deprecated) If TRUE, the resultset from the query will first be loaded from the cache. The query will be executed if a cached resultset is not retrieved for this particular query, after which the resultset will be cached. If FALSE, Athena or conn will be directly queried without any caching operations.
`render_sql`	If TRUE, the SQL will be printed back in the console prior to execution. Default: FALSE
`verbose`	If TRUE, prints loading and querying operations messages to the console. Default: FALSE
`sleepTime`	Argument for 'Sys.sleep()' in between queries to allow for halting function execution, especially in cases where other chariot functions are executing multiple queries in succession and require cancellation.

a [tibble][tibble::tibble-package]

parse_expr str_remove select_all,vars,reexports,mutate-joins

Other query functions: queryAncestors(), queryAthena(), queryCode(), queryConceptClassRelationships(), queryConceptId(), queryDescendants(), queryRelationships(), querySynonyms(), queryVocabularyRelationships(), query_athena()

library(pg13)
library(tidyverse)

conn <- local_connect("polyester")

queryCDM(sql_statement = "SELECT * FROM omop_cdm.drug_exposure ORDER BY RANDOM() LIMIT 5;",
         write_schema = "omop_cdm",
         vocab_schema = "omop_cdm",
         conn = conn)

dc(conn = conn)