Format a drug_restart object into a visual table.

Usage

tableDrugRestart(
  result,
  header = c("strata"),
  splitStrata = TRUE,
  cohortName = TRUE,
  cdmName = TRUE,
  groupColumn = c("cdm_name", "cohort_name"),
  type = "gt",
  formatEstimateName = c(`N (%)` = "<count> (<percentage> %)"),
  .options = list()
)

Arguments

result

A summarised_result object with results from summariseDrugRestart().

header

A vector containing which elements should go into the header in order. Allowed values: cdm_name, cohort_name, strata, variable, estimate.

splitStrata

If TRUE strata columns will be split.

cohortName

If TRUE cohort names will be displayed.

cdmName

If TRUE database names will be displayed.

groupColumn

Column to use as group labels. Allowed values: cdm_name, cohort_name, strata, variable_name, variable_level, estimate_name.

type

Type of desired formatted table, possibilities: "gt", "flextable", "tibble".

formatEstimateName

Named list of estimate name's to join, sorted by computation order. Indicate estimate_name's between <...>.

.options

Named list with additional formatting options. DrugUtilisation::defaultTableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of summariseDrugRestart() results.

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

conceptlist <- list("a" = 1125360, "b" = c(1503297, 1503327))
cdm <- generateDrugUtilisationCohortSet(
  cdm = cdm,
  name = "switch_cohort",
  conceptSet = conceptlist
)
#> Warning: ! 1 casted column in switch_cohort (cohort_codelist) as do not match expected
#>   column type:
#> • `concept_id` from numeric to integer

result <- cdm$cohort1 |>
  summariseDrugRestart(switchCohortTable = "switch_cohort")
#> Warning: `package_name` and `package_version` are not provided will be populated as ""
#> in settings

tableDrugRestart(result)
#> ! Results have not been suppressed.


  
Follow-up
      
Event
      
Estimate name
      
Estimate value
    
DUS MOCK; cohort_1
    
End of observation
restart
N (%)
0 (0.00 %)

switch
N (%)
0 (0.00 %)

restart and switch
N (%)
0 (0.00 %)

not treated
N (%)
1 (100.00 %)
DUS MOCK; cohort_2
    
End of observation
restart
N (%)
0 (0.00 %)

switch
N (%)
0 (0.00 %)

restart and switch
N (%)
0 (0.00 %)

not treated
N (%)
3 (100.00 %)
DUS MOCK; cohort_3
    
End of observation
restart
N (%)
0 (0.00 %)

switch
N (%)
0 (0.00 %)

restart and switch
N (%)
0 (0.00 %)

not treated
N (%)
6 (100.00 %)

CDMConnector::cdmDisconnect(cdm = cdm)
# }