Summarise code use from achilles counts

Usage

summariseAchillesCodeUse(x, cdm, countBy = c("record", "person"))

Arguments

x: Codelist
cdm: cdm_reference via CDMConnector::cdm_from_con()
countBy: Either "record" for record-level counts or "person" for person-level counts

Value

A tibble with results

Examples

# \donttest{
cdm <- mockVocabRef("database")
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 3 column in observation_period do not match expected column type:
#> • `observation_period_id` is numeric but expected integer
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: ! 8 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 1 column in vocabulary do not match expected column type:
#> • `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 3 column in concept_relationship do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 1 column in concept_synonym do not match expected column type:
#> • `language_concept_id` is logical but expected integer
#> Warning: ! 2 column in concept_ancestor do not match expected column type:
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 7 column in drug_strength do not match expected column type:
#> • `amount_value` is logical but expected numeric
#> • `amount_unit_concept_id` is numeric but expected integer
#> • `numerator_unit_concept_id` is numeric but expected integer
#> • `denominator_unit_concept_id` is numeric but expected integer
#> • `box_size` is logical but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> Warning: ! 8 column in achilles_analysis do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `analysis_name` is numeric but expected character
#> • `stratum_1_name` is logical but expected character
#> • `stratum_2_name` is logical but expected character
#> • `stratum_3_name` is logical but expected character
#> • `stratum_4_name` is logical but expected character
#> • `stratum_5_name` is logical but expected character
#> • `category` is logical but expected character
#> Warning: ! 7 column in achilles_results do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `stratum_1` is numeric but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> • `count_value` is numeric but expected integer
#> Warning: ! 16 column in achilles_results_dist do not match expected column type:
#> • `analysis_id` is numeric but expected integer
#> • `stratum_1` is logical but expected character
#> • `stratum_2` is logical but expected character
#> • `stratum_3` is logical but expected character
#> • `stratum_4` is logical but expected character
#> • `stratum_5` is logical but expected character
#> • `min_value` is logical but expected integer
#> • `max_value` is logical but expected integer
#> • `avg_value` is logical but expected numeric
#> • `stdev_value` is logical but expected numeric
#> • `median_value` is logical but expected numeric
#> • `p10_value` is logical but expected numeric
#> • `p25_value` is logical but expected numeric
#> • `p75_value` is logical but expected numeric
#> • `p90_value` is logical but expected numeric
#> • `count_value` is numeric but expected integer
#> Warning: There are observation period end dates after the current date: 2024-11-11
#> ℹ The latest max observation period end date found is 2025-12-31
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 3 column in observation_period do not match expected column type:
#> • `observation_period_id` is numeric but expected integer
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: There are observation period end dates after the current date: 2024-11-11
#> ℹ The latest max observation period end date found is 2025-12-31
oa <- getCandidateCodes(cdm = cdm, keywords = "osteoarthritis")
#> Limiting to domains of interest
#> Getting concepts to include
#> Adding descendants
#> Search completed. Finishing up.
#> ✔ 2 candidate concepts identified
#> Time taken: 0 minutes and 0 seconds
result_achilles <- summariseAchillesCodeUse(list(oa = oa$concept_id), cdm = cdm)
#> 
result_achilles
#> # 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 oa          domain_id   condition   
#> 2         1 mock     codelist_name oa          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)
# }