Skip to contents

Using generateSequenceCohortSet to obtain sequence ratios for the desired outcomes.

Usage

summariseSequenceRatios(
  cohort,
  cohortId = NULL,
  confidenceInterval = 95,
  minCellCount = 5
)

Arguments

cohort

A cohort table in the cdm.

cohortId

The Ids in the cohort that are to be included in the analyses.

confidenceInterval

Default is 95, indicating the central 95% confidence interval.

minCellCount

The minimum number of events to reported, below which results will be obscured. If 0, all results will be reported.

Value

A local table with all the analyses.

Examples

# \donttest{
library(CohortSymmetry)
cdm <- mockCohortSymmetry()
#> Warning: ! 9 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
#>  `cdm_version` is numeric but expected character
#>  `vocabulary_version` is logical but expected character
#> Warning: ! 3 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
#> Warning: ! 1 column in vocabulary do not match expected column type:
#>  `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 5 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
#>  `valid_start_date` is logical but expected date
#>  `valid_end_date` is logical but expected date
#>  `invalid_reason` is logical but expected character
#> Warning: ! 2 column in concept_synonym do not match expected column type:
#>  `concept_id` is numeric but expected integer
#>  `language_concept_id` 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_value` is logical but expected numeric
#>  `denominator_unit_concept_id` is numeric but expected integer
#>  `box_size` is numeric but expected integer
#>  `valid_start_date` is character but expected date
#>  `valid_end_date` is character but expected date
#> Warning: There are observation period end dates after the current date: 2024-11-15
#>  The latest max observation period end date found is 2026-10-26
#> Warning: There are observation period end dates after the current date: 2024-11-15
#>  The latest max observation period end date found is 2026-10-26
cdm <- generateSequenceCohortSet(cdm = cdm,
                                 name = "joined_cohorts",
                                 indexTable = "cohort_1",
                                 markerTable = "cohort_2")
pssa_result <- summariseSequenceRatios(cohort = cdm$joined_cohorts, minCellCount = 0)
#> Warning: For at least some combinations, index is always before marker or marker always
#> before index
#> -- 5 combinations of 8 had index always before marker
#> -- 5 combinations of 8 had marker always before index
#> Warning: `cdm_name` is present in both 'settings' and 'summarised_result'. This will be
#> an error in the next release.
#> Warning: `cdm_name` is present in both 'settings' and 'summarised_result'. This will be
#> an error in the next release.
#> Warning: `cdm_name` is present in both 'settings' and 'summarised_result'. This will be
#> an error in the next release.
pssa_result
#> # A tibble: 80 × 13
#>    result_id cdm_name      group_name       group_level strata_name strata_level
#>        <int> <chr>         <chr>            <chr>       <chr>       <chr>       
#>  1         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  2         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  3         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  4         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  5         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  6         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  7         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  8         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#>  9         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#> 10         1 mock database index_cohort_na… cohort_1 &… overall     overall     
#> # ℹ 70 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>
CDMConnector::cdmDisconnect(cdm)
# }