![[Experimental]](figures/lifecycle-experimental.svg)
Usage
summariseDrugRestart(
cohort,
switchCohortTable,
switchCohortId = NULL,
strata = list(),
followUpDays = Inf,
censorDate = NULL,
restrictToFirstDiscontinuation = TRUE
)Arguments
- cohort
A cohort table.
- switchCohortTable
A cohort table in the cdm that contains possible alternative treatments.
- switchCohortId
The cohort ids to be used from switchCohortTable. If NULL all cohort definition ids are used.
- strata
List with column names or vectors of column names groups to stratify results by.
- followUpDays
A vector of number of days to follow up. It can be multiple values.
- censorDate
Date of censoring. Individuals are always censored at the end of observation.
- restrictToFirstDiscontinuation
Whether to consider only the first discontinuation episode or all of them.
Value
A summarised_result object with the percentages of restart, switch and not exposed per window.
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)
#> Warning: The `split` argument of `visOmopTable()` is deprecated as of visOmopResults
#> 0.4.0.
#> ℹ The deprecated feature was likely used in the DrugUtilisation package.
#> Please report the issue at
#> <https://github.com/darwin-eu/DrugUtilisation/issues>.
#> ! Results have not been suppressed.
DUS MOCK; cohort_1
DUS MOCK; cohort_2
DUS MOCK; cohort_3
CDMConnector::cdmDisconnect(cdm = cdm)
# }