A plot for the temporal symmetry of cohorts.
Source:R/plotTemporalSymmetry.R
plotTemporalSymmetry.Rd
It provides a ggplot of the temporal symmetry of two or more cohorts.
Arguments
- result
Table output from summariseTemporalSymmetry.
- plotTitle
Title of the plot, if NULL no title will be plotted.
- labs
Axis labels for the plot.
- xlim
Limits for the x axis of the plot.
- colours
Colours for both parts of the plot, pre- and post- time 0.
- scales
Whether to set free y scales for the facet wrap when there are multiple plots (i.e. each plot has its own scaled y axis) or set them equal for all. Only accepts "free" for the former and "fixed" for the latter.
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")
temporal_symmetry <- summariseTemporalSymmetry(cohort = cdm$joined_cohort,
minCellCount = 0)
#> 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.
plotTemporalSymmetry(result = temporal_symmetry)
#> Warning: `cdm_name` is present in both 'settings' and 'summarised_result'. This will be
#> an error in the next release.
CDMConnector::cdmDisconnect(cdm = cdm)
# }