It provides a ggplot of the sequence ratios of index and marker cohorts.
Examples
# \donttest{
library(CohortSymmetry)
cdm <- mockCohortSymmetry()
#> Warning: ! 6 column in person do not match expected column type:
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `month_of_birth` 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
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `period_type_concept_id` is numeric but expected integer
#> 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: 2024-09-23
#> ℹ The latest max observation period end date found is 2026-10-26
#> Warning: ! 6 column in person do not match expected column type:
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `month_of_birth` 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
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: There are observation period end dates after the current date: 2024-09-23
#> ℹ The latest max observation period end date found is 2026-10-26
cdm <- generateSequenceCohortSet(cdm = cdm,
indexTable = "cohort_1",
markerTable = "cohort_2",
name = "joined_cohort")
sequence_ratio <- summariseSequenceRatios(cohort = cdm$joined_cohort,
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.
plotSequenceRatios(result = sequence_ratio)
#> Warning: `cdm_name` is present in both 'settings' and 'summarised_result'. This will be
#> an error in the next release.
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_errorbarh()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_point()`).
CDMConnector::cdmDisconnect(cdm = cdm)
# }