Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient

Usage

summariseDoseCoverage(
  cdm,
  ingredientConceptId,
  estimates = c("count_missing", "percentage_missing", "mean", "sd", "q25", "median",
    "q75"),
  sampleSize = NULL
)

Arguments

cdm: A cdm reference created using CDMConnector.
ingredientConceptId: Code indicating the ingredient of interest.
estimates: Estimates to obtain.
sampleSize: Maximum number of records of an ingredient to estimate dose coverage. If an ingredient has more, a random sample equal to sampleSize will be considered. If NULL, all records will be used.

Value

The function returns information of the coverage of computeDailyDose.R for the selected ingredients and concept sets

Examples

# \donttest{
library(DrugUtilisation)

cdm <- mockDrugUtilisation()
#> Warning: ! 6 column in person do not match expected column type:
#> • `gender_concept_id` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> • `location_id` is numeric but expected integer
#> • `provider_id` is numeric but expected integer
#> • `care_site_id` is numeric but expected integer
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: ! 2 column in visit_occurrence do not match expected column type:
#> • `visit_concept_id` is numeric but expected integer
#> • `visit_type_concept_id` is numeric but expected integer
#> Warning: ! 10 column in condition_occurrence do not match expected column type:
#> • `condition_concept_id` is numeric but expected integer
#> • `condition_type_concept_id` is numeric but expected integer
#> • `condition_status_concept_id` is numeric but expected integer
#> • `stop_reason` is logical but expected character
#> • `provider_id` is logical but expected integer
#> • `visit_occurrence_id` is logical but expected integer
#> • `visit_detail_id` is logical but expected integer
#> • `condition_source_value` is logical but expected character
#> • `condition_source_concept_id` is logical but expected integer
#> • `condition_status_source_value` is logical but expected character
#> Warning: ! 2 column in drug_exposure do not match expected column type:
#> • `drug_concept_id` is numeric but expected integer
#> • `drug_type_concept_id` is numeric but expected integer
#> Warning: ! 2 column in observation do not match expected column type:
#> • `observation_concept_id` is numeric but expected integer
#> • `observation_type_concept_id` is numeric but expected integer
#> Warning: ! 4 column in concept do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 2 column in concept_relationship do not match expected column type:
#> • `concept_id_1` is numeric but expected integer
#> • `concept_id_2` is numeric but expected integer
#> Warning: ! 4 column in concept_ancestor do not match expected column type:
#> • `ancestor_concept_id` is numeric but expected integer
#> • `descendant_concept_id` is numeric but expected integer
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 9 column in drug_strength do not match expected column type:
#> • `drug_concept_id` is numeric but expected integer
#> • `ingredient_concept_id` is numeric but expected integer
#> • `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 character but expected date
#> • `valid_end_date` is character but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 6 column in person do not match expected column type:
#> • `gender_concept_id` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> • `location_id` is numeric but expected integer
#> • `provider_id` is numeric but expected integer
#> • `care_site_id` is numeric but expected integer
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `period_type_concept_id` is numeric but expected integer

summariseDoseCoverage(cdm, 1125315)
#> ℹ The following estimates will be computed:
#> • daily_dose: count_missing, percentage_missing, mean, sd, q25, median, q75
#> ! Table is collected to memory as not all requested estimates are supported on
#>   the database side
#> → Start summary of data, at 2024-09-10 15:03:19.969374
#> ✔ Summary finished, at 2024-09-10 15:03:20.253599
#> # A tibble: 56 × 13
#>    result_id cdm_name group_name      group_level   strata_name strata_level
#>        <int> <chr>    <chr>           <chr>         <chr>       <chr>       
#>  1         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  2         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  3         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  4         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  5         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  6         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  7         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  8         1 DUS MOCK ingredient_name acetaminophen overall     overall     
#>  9         1 DUS MOCK ingredient_name acetaminophen unit        milligram   
#> 10         1 DUS MOCK ingredient_name acetaminophen unit        milligram   
#> # ℹ 46 more rows
#> # 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>
# }