Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations

Usage

summariseOrphanCodes(
  x,
  cdm,
  domain = c("condition", "device", "drug", "measurement", "observation", "procedure",
    "visit")
)

Arguments

x: A codelist for which to find related codes used in the database
cdm: cdm_reference via CDMConnector
domain: The domains to restrict results too. Only concepts from these domains will be returned.

Value

A summarised result containg the frequency of codes related to (but not in) the codelist

Examples

# \donttest{
cdm <- mockVocabRef("database")
#> Warning: There are observation period end dates after the current date: 2025-02-19
#> ℹ The latest max observation period end date found is 2025-12-31
#> Warning: There are observation period end dates after the current date: 2025-02-19
#> ℹ The latest max observation period end date found is 2025-12-31
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)
#> Limiting to domains of interest
#> Getting concepts to include
#> Search completed. Finishing up.
#> ✔ 1 candidate concept identified
#> Time taken: 0 minutes and 0 seconds

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)
#> PHOEBE results not available
#> ℹ The concept_recommended table is not present in the cdm.
#> Getting orphan codes for msk
#> 

orphan_codes
#> # A tibble: 2 × 13
#>   result_id cdm_name group_name    group_level strata_name strata_level
#>       <int> <chr>    <chr>         <chr>       <chr>       <chr>       
#> 1         1 mock     codelist_name msk         domain_id   condition   
#> 2         1 mock     codelist_name msk         domain_id   condition   
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> #   estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> #   additional_name <chr>, additional_level <chr>
CDMConnector::cdmDisconnect(cdm)
# }