A plot for the sequence ratios.

It provides a ggplot of the sequence ratios of index and marker cohorts.

Usage

plotSequenceRatios(
  result,
  onlyaSR = FALSE,
  plotTitle = NULL,
  labs = c("SR", "Drug Pairs"),
  colours = c("red", "blue")
)

Arguments

result

Table output from summariseSequenceRatios.

onlyaSR

If the only SR to be plotted is the adjusted SR.

plotTitle

Title of the plot, if NULL no title will be plotted.

labs

Axis labels for the plot.

colours

Colours for both parts of the plot, pre- and post- time 0.

Value

A plot for the sequence ratios of index and marker cohorts.

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
#> ℹ 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
#> 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 2 rows containing missing values or values outside the scale range
#> (`geom_errorbarh()`).
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_point()`).

CDMConnector::cdmDisconnect(cdm = cdm)
# }