Search for a Code in the Concept Table

search_code(
  code_pattern,
  ignore.case = FALSE,
  perl = FALSE,
  fixed = FALSE,
  useBytes = FALSE,
  vocab_schema = "omop_vocabulary",
  limit = NULL,
  conn,
  conn_fun = "connectAthena()",
  cache_only = FALSE,
  skip_cache = FALSE,
  override_cache = FALSE,
  verbose = TRUE,
  render_sql = TRUE,
  sleepTime = 1
)

Arguments

code_pattern	Regex pattern of code
conn	Connection object. If provided, diverts queries to the connection instead of the local Athena instance without caching features.
cache_only	Loads from the cache and does not query the database. A NULL object is returned if a resultset was not cached.
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.
verbose	If TRUE, prints loading and querying operations messages to the console. Default: FALSE
render_sql	If TRUE, the SQL will be printed back in the console prior to execution. 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.

Value

resultset as a dataframe with all column types as character and trimmed white space

Examples

if(interactive()){
 search_code(code_pattern = "^C40")
 }
#> [2021-05-26 16:07:39]	Connected to 'athena'
#> [2021-05-26 16:07:39]	Loading Cache...
#> [2021-05-26 16:07:39]	Cached SQL: SELECT *
#> FROM omop_vocabulary.concept
#> WHERE LOWER(concept_code) LIKE '%%c40%'
#> [2021-05-26 16:07:39]	Cached resultset found...
#> [2021-05-26 16:07:39]	Postgres connection to 'athena' closed
#> # A tibble: 179 x 10
#>    concept_id concept_name              domain_id vocabulary_id concept_class_id
#>         <int> <chr>                     <chr>     <chr>         <chr>           
#>  1     705913 prucalopride              Drug      MeSH          Suppl Concept   
#>  2     979962 mintlactone               Drug      MeSH          Suppl Concept   
#>  3    1036764 2-methoxy-4-prop-1-enylp… Drug      MeSH          Suppl Concept   
#>  4    1405897 Malignant neoplasm of bo… Condition ICD10CN       ICD10 Hierarchy 
#>  5    1405898 Malignant neoplasm: Scap… Condition ICD10CN       ICD10 code      
#>  6    1405899 Malignant neoplasm: Scap… Condition ICD10CN       ICD10 code      
#>  7    1405900 Scapula cancer (machine … Condition ICD10CN       ICD10 code      
#>  8    1405901 Humerus cancer (machine … Condition ICD10CN       ICD10 code      
#>  9    1405902 Ulna cancer (machine tra… Condition ICD10CN       ICD10 code      
#> 10    1405903 Radial bone cancer (mach… Condition ICD10CN       ICD10 code      
#> # … with 169 more rows, and 5 more variables: standard_concept <chr>,
#> #   concept_code <chr>, valid_start_date <date>, valid_end_date <date>,
#> #   invalid_reason <chr>